https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=PohlNAMIC Wiki - User contributions [en]2026-04-17T00:45:36ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=717832011 Slicer4-PreRSNAHackFest2011-11-08T07:52:05Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits) ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{In Progress}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| KP<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| JC<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| SP<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1516 1516]<br />
| JC<br />
| ctkVTKErrorLogMessageHandler crashes<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1517 1517]<br />
| KP<br />
| Preprocessing returns inconsistent scalar volume<br />
|-<br />
| {{done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1518 1518]<br />
| HJ<br />
| BRAINS is called but nothing happens<br />
|-<br />
| {{In Progress}}<br />
| <br />
| SP<br />
| Slow DICOM Query/Retrieve with XNAT Gateway<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=717782011 Slicer4-PreRSNAHackFest2011-11-07T19:43:57Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits) ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{In Progress}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| KP<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| JC<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| SP<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1516 1516]<br />
| JC<br />
| ctkVTKErrorLogMessageHandler crashes<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1517 1517]<br />
| KP<br />
| Preprocessing returns inconsistent scalar volume<br />
|-<br />
| {{done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1518 1518]<br />
| HJ<br />
| BRAINS is called but nothing happens<br />
|-<br />
| {{In Progress}}<br />
| <br />
| SP<br />
| Slow DICOM Query/Retrieve with XNAT Gateway<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=717672011 Slicer4-PreRSNAHackFest2011-11-07T05:48:31Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits) ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{In Progress}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{In Progress}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| KP<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| JC<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| SP<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1516 1516]<br />
| JC<br />
| ctkVTKErrorLogMessageHandler crashes<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1517 1517]<br />
| KP<br />
| Preprocessing returns inconsistent scalar volume<br />
|-<br />
| {{In Progress}}<br />
| [http://na-mic.org/Mantis/view.php?id=1518 1518]<br />
| HJ<br />
| BRAINS is called but nothing happens<br />
|-<br />
| {{In Progress}}<br />
| <br />
| SP<br />
| Slow DICOM Query/Retrieve with XNAT Gateway<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=717352011 Slicer4-PreRSNAHackFest2011-11-03T20:59:51Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits) ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| KP<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| JC<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| SP<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1516 1516]<br />
| JC<br />
| ctkVTKErrorLogMessageHandler crashes<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1517 1517]<br />
| KP<br />
| Preprocessing returns inconsistent scalar volume<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1518 1518]<br />
| HJ<br />
| BRAINS is called but nothing happens<br />
|-<br />
| {{Not Done}}<br />
| <br />
| SP<br />
| Slow DICOM Query/Retrieve with XNAT Gateway<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=717052011 Slicer4-PreRSNAHackFest2011-11-03T18:31:13Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits) ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| KP<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| JC<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| SP<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1516 1516]<br />
| JC<br />
| ctkVTKErrorLogMessageHandler crashes<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1517 1517]<br />
| KP<br />
| Preprocessing returns inconsistent scalar volume<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1518 1518]<br />
| HJ<br />
| BRAINS is called but nothing happens<br />
|-<br />
| {{Not Done}}<br />
| <br />
| SP<br />
| Slow DICOM Query/Retrieve with XNAT Gateway<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716922011 Slicer4-PreRSNAHackFest2011-11-02T21:09:14Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| Jc<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| HJ<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| SP<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1516 1516]<br />
| JC<br />
| ctkVTKErrorLogMessageHandler crashes<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1517 1517]<br />
| KP<br />
| Preprocessing returns inconsistent scalar volume<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1518 1518]<br />
| HJ<br />
| BRAINS is called but nothing happens<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716882011 Slicer4-PreRSNAHackFest2011-11-02T16:53:39Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| Jc<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| HJ<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| Steve<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1516 1516]<br />
| JC<br />
| ctkVTKErrorLogMessageHandler crashes<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1517 1517]<br />
| KP<br />
| Preprocessing returns inconsistent scalar volume<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716872011 Slicer4-PreRSNAHackFest2011-11-02T16:53:20Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| Jc<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| HJ<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| Steve<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1516 1516]<br />
| JC<br />
| ctkVTKErrorLogMessageHandler crashes<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1517 1517]<br />
| Kilian<br />
| Preprocessing returns inconsistent scalar volume<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716862011 Slicer4-PreRSNAHackFest2011-11-02T16:21:40Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| Jc<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| HJ<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1515 1515]<br />
| Steve<br />
| Labelmaps generated by EMSegmenter Fast cannot be edited <br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716852011 Slicer4-PreRSNAHackFest2011-11-02T15:59:24Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| Jc<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| HJ<br />
| BRAINS not available in MAC package <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1513 1513]<br />
| KP<br />
| EMSegmenter Fast: Incorrect labels in Step 3<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716842011 Slicer4-PreRSNAHackFest2011-11-02T15:54:44Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1498 1498]<br />
| Jc<br />
| EMSegmenter Tasks are not found in Windows build <br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| HJ<br />
| BRAINS not available in MAC package <br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716832011 Slicer4-PreRSNAHackFest2011-11-02T15:47:35Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| HJ<br />
| BRAINS not available in MAC package <br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716822011 Slicer4-PreRSNAHackFest2011-11-02T15:47:20Z<p>Pohl: /* Issues */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1506 1506]<br />
| HJ<br />
| BRAINS not available in MAC package <br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=2011_Slicer4-PreRSNAHackFest&diff=716812011 Slicer4-PreRSNAHackFest2011-11-02T15:44:55Z<p>Pohl: /* Participants */</p>
<hr />
<div>=What=<br />
Slicer 4 PreRSNA Sprint. <br />
<br />
Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing. <br />
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.<br />
<br />
=Who=<br />
Core developers<br />
<br />
=Where= <br />
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer<br />
<br />
=When=<br />
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]<br />
<br />
=Participants=<br />
<!-- Alphabetically sorted list --><br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Participants'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Name<br />
! scope=col style="background:#cde6f8;"| Available Operating System<br />
! scope=col style="background:#cde6f8;"| Remarks<br />
|-<br />
| Nicole Aucoin<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jean-Christophe Fillion-Robin<br />
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?<br />
|<br />
|-<br />
| Julien Finet<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Hans Johnson<br />
| {{Not Done}}<br />
| <br />
|-<br />
| Jim Miller<br />
| Mac 64bit 10.7<br />
| <br />
|-<br />
| Steve Pieper<br />
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64<br />
| <br />
|-<br />
| Kilian Pohl<br />
| Ubuntu 11.10 64 bit trunk <br />
| <br />
|}<br />
<br />
=Issues=<br />
{{note}}''Describe the issue shortly and add the corresponding mantis link.''<br />
<br />
{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"<br />
|+ '''''Issues'''''<br />
|-<br />
! scope=col style="background:#cde6f8;"| Progress<br />
! scope=col style="background:#cde6f8;"| Issue#<br />
! scope=col style="background:#cde6f8;"| Developer<br />
! scope=col style="background:#cde6f8;"| Short description / Notes<br />
|-<br />
| {{Not Done}} <!-- DO NOT COPY THIS COMMENT: You can also use {{In Progress}} or {{Done}} --><br />
| [http://na-mic.org/Mantis/view.php?id=1375 1375]<br />
| Jc<br />
| QT_PLUGIN_PATH not set right on windows install<br />
|-<br />
| {{Not Done}}<br />
| [http://na-mic.org/Mantis/view.php?id=1464 1464]<br />
| Jc<br />
| Slicer crash while trying to call CLI module from python<br />
|}</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation&diff=67177Projects:ARRA:miAnnotation2011-05-15T16:39:56Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
<br />
= Aim =<br />
[[Image:SlicerAM_QtAnnotation.png|241px|right|Annotation Module]]<br />
<br />
Medical images often contain a wealth of information, such as anatomy and pathology, not explicitly accessible. One way to address this issue is via image annotation and markup. We propose to create a comprehensive framework for annotation and markup within 3D Slicer, enabling users to capture structured information easily. Furthermore, we will develop schemas for saving and recovering this information into and from XNAT, allowing queries of larger data sets of medical scans. This tool will provide clinicians with a relatively simple way to capture information latent in medical scans, and also to select micro-cohorts of medical scans for studying diseases.<br />
<br />
= Research Plan =<br />
3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include: <br />
* a rich set of geometric objects for improved visual differentiation between annotations<br />
* markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection<br />
* entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologiesand <br />
* a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT.<br />
<br />
We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region.<br />
<br />
The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values. <br />
<br />
Both modules are accompanied by training materials and documentation to ensure usability.<br />
=Design of Module=<br />
* Current [[Media:AMI-GUI-Design.ppt | GUI ]] outline - [[Media:SlicerAM QtAnnotation.png | Screenhot]] in Slicer <br />
* Suggested [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] outline<br />
* Wendy's Mouse Mode sketches http://www.slicer.org/slicerWiki/index.php/Slicer4:UIDesign:MouseModeSketches<br />
<br />
= Documentation=<br />
* [[ miAnnotation_Documentation | Documentation ]] of the module<br />
* Using the [[Media:Slicer4_miAnnotation.ppt | module]] with corresponding data ([[Media:Slicer4_miAnnotation_data.zip | sample data]] )<br />
<br />
=Key Personnel=<br />
10% Kilian Pohl (UPenn) <BR><br />
95% Daniel Haehn (UPenn) <BR><br />
5% Dominique Belhachemi (UPenn) <BR><br />
<br />
=Past Contributors=<br />
Yong Zhang (IBM) <br><br />
<br />
=Events=<br />
* 05/18/10 [[Media:miAnnotation_May2010_Yong.pdf | Presentation]] at the Department of Healthcare Informatics, IBM, Almaden<br />
* 12/16/09 - 12/17/09 [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]]<br />
* 01/06/10 [[AHM2010:AnnotationBreakout | Break out session]] at AHM 2010<br />
* 01/19/10 Biweekly Annotation Tcon from 4:00 - 5:00 pm EST (next meeting 2/9): Tel: (218) 862-1115 Conference ID: 348265#, [https://www.lotuslive.com/join?schedid=4572317 Desktop Sharing ]<br />
* 08/30/10 Budget Year 1 [[ Projects:ARRA:SlicerAM:Meeting20100831 | Review meeting ]]<br />
<br />
=Progress=<br />
* 05/13/11<br />
** MRML: add required modified events for certain display properties<br />
** add opacity slider to text properties in the property dialog<br />
** add a spacer to the property dialog to have a consistent design for text, point and line properties<br />
** add label position to the display node<br />
** add utility methods to get the text, point, line display nodes for a given mrml node id<br />
** handle the main annotation types when setting them active in the selection node<br />
** hook up the text opacity, the point material properties. Grey out the line tab if no line display node. Add the point values to the table in the points tab<br />
** removed the Save panel from the module GUI and moved the buttons for report and screenshot in the edit toolbar (this might change at one point)<br />
** added a storage node for the annotation screen snapshot node to properly save the screenshots<br />
** cleanup of annotation snapshot nodes<br />
** use the text opacity, the point material properties<br />
** add value constraints for several sliders in the property dialog<br />
** MRML: add new method SetControlPoint(id, coords) without the visible and selected flags<br />
** property dialog now complete for text, point, line! (not for hierarchies yet)<br />
* 05/06/11<br />
** fiducials are now shown the same way in 2D and 3D<br />
** the property dialog is connected to configure point colors and glyph types for fiducials<br />
** it is possible to add text to a fiducial in 3D<br />
** meeting with Ron to discuss further development and usability issues<br />
* 04/29/11<br />
** fixed the flickering when placing or interacting with fiducials and rulers<br />
** removed some obsolete render calls to enhance performance<br />
* 04/22/11<br />
** worked together with Nicole<br />
*** finally fixed the crash on Slicer exit<br />
*** investigated why MRMLScene import works fine with the annotations but MRMLScene load does not<br />
**** first success: import and load mrml scenes now both load the annotations in 2D and 3D<br />
* 04/15/11<br />
** Maintenance<br />
* 04/08/11<br />
** Maintenance<br />
* 04/01/11<br />
** Maintenance<br />
* 03/25/11<br />
** Maintenance<br />
* 03/18/11<br />
** Work on MRML Load/Save issues (Nicole)<br />
** Maintenance<br />
* 03/11/11<br />
** Work on hierarchies (Nicole)<br />
** Maintenance<br />
* 03/04/11<br />
** Maintenance<br />
* 02/25/11<br />
** Maintenance<br />
* 02/18/11<br />
** Maintenance<br />
** Communication with Daniel Rubin from Stanford to plan AIM integration<br />
*** provided Annotation MRML examples<br />
* 02/11/11<br />
** Maintenance<br />
* 02/04/11<br />
** Clarified how to add Node Selectors for Annotations to the GUI of 3rd Party 3D Slicer Modules<br />
*** Kitware provided necessary infrastructure<br />
*** Proof of Concept in the new CropVolume module with ROI Annotations (Andriy)<br />
** Clearing up the Annotation Storage Node Tests (Nicole)<br />
* 01/28/11<br />
** Presented Annotation module and SceneView module at NAC EAB Meeting<br />
** Smaller bugs and maintenance<br />
** Meeting with Nicole and Alex concerning the final API of hierarchies in Slicer4<br />
* 01/21/11<br />
** Re-activated ROI annotation with backwards compatibility to the old vtkMRMLROINode<br />
*** Tested successfully with a scene from Slicer3<br />
*** Provided documentation to relevant people<br />
** Rulers now support the measurement tape behavior<br />
** Changed the UPenn logo<br />
** Several smaller fixes<br />
** provided Wendy with Screenshots for NAC Poster<br />
*** [[File:Annotation.png|none|thumb|The current state of the Annotation module.]]<br />
*** [[File:Report.png|none|thumb|The report dialog.]]<br />
** Found displayableManager inconsistency between 2D and 3D and the MRML Node Added Event<br />
** MRML backwards compatibility fix for all Annotations<br />
*** new tag "visible", old tag "visibility"<br />
* 01/14/11<br />
** Attended NA-MIC project week<br />
**Enabled picking when placing annotations in 3D. <br />
**Fixed display of ruler intersections. <br />
**Added new icons. <br />
**Use only three seeds to place bidimensional widgets which results in more stability. <br />
**It is also now possible to add annotations to the toplevel hierarchy after another hierarchy was created by clicking in an empty space of the treeView.<br />
**Re-added the ROI functionality, so now we have 5 widgets<br />
**Ruler: enabled display of ticks (measuring tape mode) in 2D and 3D<br />
* 01/07/11<br />
** re-factored the annotation module in terms of changes in the Slicer4 environment<br />
*** ready for the new developer release<br />
** worked on the outsourced SceneView functionality to make SceneViews survive round-trips (mrml load and save)<br />
* 12/31/10<br />
** Maintenance<br />
** Documentation<br />
* 12/24/10<br />
** Maintenance<br />
** Received the first bug reports of potential users<br />
*** Updated bugtracker<br />
* 12/17/10<br />
** Extended Report functionality<br />
*** now includes screenshots<br />
*** shows the hierarchies<br />
** Sorting of Annotations now possible<br />
** Widgets:<br />
*** added the 3D representation of rulers<br />
*** removed the vtkInteractorRecorder hack by placing the widgets programmatically<br />
** Outsourced the former integrated scene snapshot functionality<br />
*** Wrote a new module called SceneViews<br />
*** vtkMRMLSceneViewNode replaces the old snapshot node and includes thumbnail, description..<br />
**** is not part of the displayable framework anymore<br />
** Added confirmation questions prior to removing annotations<br />
** Worked on MRML save/load<br />
** Updated the priority list: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
** Added a section for known issues: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation#Known_issues<br />
** Annotation module Lines of Code (without .ui files and no blank lines): 24820<br />
* 12/10/10<br />
** Changed some things in the MRML architecture to enhance encapsulation<br />
*** Adding new Annotations should be easier now<br />
** Lock selected, toggle visibility of selected and delete selected implemented<br />
** Report functionality works again<br />
*** Added support to print and export as a HTML report<br />
* 12/03/10<br />
** Added icons to the hierarchy tree<br />
** Configured a proxy model to display only vtkMRMLAnnotationHierarchyNodes and vtkMRMLAnnotationNodes in the hierarchy tree<br />
** Smaller layout fixes<br />
** Added 'full layout' thumbnail functionality to Annotation snapshots<br />
** Removed the old table and replaced fully by the treeView<br />
** Over 1000 of lines of code were removed<br />
*** Hierarchies are now usable<br />
*** [[File:Annotationscreenshot.png|none|thumb|Screenshot of an example Annotation using the new features]]<br />
* 11/26/10<br />
** Added functionality to the module logic to be able to place fiducials programmatically<br />
*** This will be used if one presses the 'p' key on a slice view<br />
** Re-activated the text annotation<br />
*** Used vtkCaptionWidget instead vtkTextWidget to be able to have an anchorpoint in 3D space<br />
** The scene, camera and view nodes are now hidden from the hierarchy tree<br />
*** The toplevel annotation hierarchy is the new root and also hidden<br />
** Added functionality to show Annotation snapshot nodes in the hierarchy tree<br />
*** This required adding the original snapshot node to the displayable framework (as a workaround)<br />
*** Later, we will add thumbnail and description directly to vtkMRMLNode, so that a screenshot can be attached to every MRML node<br />
** Overall code polishing in terms of code conventions<br />
*** including the destruction of the frozen seedWidget on Slicer exit<br />
* 11/19/10<br />
** Small fixes to the Annotation snapshot functionality<br />
** New functionality: reset view to when the annotation was placed<br />
** Derived qMRMLAnnotationTreeWidget and qMRMLSceneAnnotationModel to support hierarchies in the module<br />
*** the widgets let us customize the look and feel of the treeWidget<br />
*** in this context, fixed the creation of hierarchies to a specific order in the scene (which is need for the widget)<br />
*** the Annotation hierarchy nodes and the Annotations get already displayed in the treeWidget<br />
** Fixed stack smashing in connection with a recently introduced compiler flag<br />
* 11/12/10<br />
** All widgets are now restricted to the current renderer which makes the interaction more robust.<br />
** Fixed funky behavior after fiducials were placed.<br />
** New functionality: Annotation snapshots (screenshot + description + scene snapshot) implemented.<br />
*** [[File:snapshot1.png|none|thumb|The new annotation snapshot functionality (part 1)]] [[File:snapshot2.png|none|thumb|The new annotation snapshot functionality (part 2)]]<br />
* 11/05/10<br />
** Widget Design Fiesta http://www.na-mic.org/Wiki/index.php/WidgetDesign2010<br />
** Widget intersections works nearly perfectly<br />
*** Unfortunately, only for centered datasets<br />
** Restrict ruler placement to the current renderer works now. This means, the ruler does not disappear when one point moves outside the sliceview.<br />
* 10/29/10<br />
** Lightbox view works for Fiducials<br />
*** Other widgets have to be refined to be used in a lightbox view due to inconsistent VTK API. The VTK Widget Fiesta should target this.<br />
** Widget intersections in the works, not perfectly working yet.<br />
* 10/22/10<br />
** Priority list for the December release of Slicer4: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
* 10/15/10<br />
** Adopting the old TCL logic to enable 2D widgets on reformats and lightbox views<br />
*** Still working on the lightbox view (very close)<br />
* 10/08/10<br />
** Code-cleanup of the logic class - any old and clumsy code was removed.<br />
** Introducing the StringHolder design pattern [(c) Steve] to always show measurement correctly in the GUI.<br />
** Widget creation now works on Unix aswell.<br />
** Added the RegisterNodes method to register node classes when the scene gets attached to the logic class.<br />
** Hierarchy nodes get added when an annotation is created (code workflow to be optimized).<br />
** Configured a nightly build system to build and test the annotation code every night on a SPL workstation.<br />
* 10/01/10<br />
** The hierarchy changes will replace the table in the GUI with a tree widget<br />
*** Added a tree widget to the GUI additionally to the table to display both during the transition stage<br />
** Fixed the follower bug, which sometimes dragged the second controlpoint of a widget behind when the other controlpoint was moved.<br />
* 9/24/10<br />
** Wrote performance test for vtkWidgets in a standalone VTK mode<br />
*** compared performance in Slicer against standalone VTK<br />
*** rendering of text labels was found to be the performance hog, disabling these labels increases performance inside and outside Slicer dramatically<br />
** Meeting between Wendy, Nicole, Steve and Daniel to review the Annotation module status<br />
*** Notes: [[Projects:ARRA:SlicerAM:Meeting20100921]]<br />
** Annotation hierarchy in the works<br />
* 9/17/10<br />
** 2D placement of Rulers, Bidimensional and Fiducials works now<br />
*** The widgets get synchronized along the slice viewers and the 3D view<br />
** Added extra layer on top of vtkWidgets and vtkWidgetRepresentations to add some extra functionality like calculating distances of measurement correctly in 2D<br />
*** bidimensional measurement and rulers now show the correct distance also in 2D<br />
** Fixed possible null pointer exception in vtkMRMLSliceLogic<br />
** Refactored GetSliceOffSet from vtkMRMLSliceLogic to vtkMRMLSliceNode<br />
* 9/10/10<br />
** 2D placement of Annotations in the works<br />
*** change of the underlying architecture to use one displayableManager for 2D and 3D resulting in less code duplication<br />
*** to perform the changes, all annotations but fiducials were disabled for now<br />
* 9/3/10<br />
** Annotation module status review and planning meeting took place in 1249 Boylston<br />
*** Agenda and Notes: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:Meeting20100831<br />
**** includes new generated class diagram<br />
** Property dialog updated (see screenshot)<br />
*** [[File:Annotationpropertydialog.png|none|thumb|The new annotation property dialog.]]<br />
*** first MRML-Widget synchronization works, the text tab in the property dialog works well with the text widget<br />
** new icons for bidimensional measurement and ROI by Wendy<br />
** updated ctkColorPickerButton to include the ability to disable the setting of the color hexcode as the buttontext to avoid the workaround we had in the annotation module<br />
* 08/27/10<br />
** added a work-around to initialize renderer properly resulting in improved display of annotations in 3D viewer<br />
** cleaned up the code (more then 1000 lines of code where obsolete)<br />
** updating property dialog, which includes revisiting the displayableManagers to support MRML and widget updates<br />
* 08/20/10<br />
** fiducials and sticky node work now<br />
** ruler and spline work now<br />
*** spline widget causes problems b/c after one spline was placed, no interaction with 3D scene possible<br />
** ROI works now<br />
** all annotations now can be placed to examine widget behavior<br />
** started working on a new interface for the property dialog<br />
** consolidated experts for 2D slice displayableManagers<br />
** started working on synchronizing the widgets with MRML display nodes<br />
** fixed GUI problem: the table did not expand even if there was free space in the module frame. now it works.<br />
* 08/13/10<br />
** Wendy, Nicole and Daniel discussed how to integrate mouse modes of Slicer into Annotation module and vice versa. Solution is a widget which appears in the Annotation module panel but can also be shown outside of it as a toplevel window in Slicer (maybe with keybinding), see here: http://wiki.na-mic.org/Wiki/index.php/File:Widget.png<br />
** current status (workflow, user places seeds and widget appears):<br />
*** angle annotations work (note: the widget did not support programmatical placement. a trick is used to place the widget where the user has clicked)<br />
*** text annotations work<br />
** modified vtkMRMLInteractionNode to have a customTag for place modes not only from annotation module but all modules<br />
* 08/06/10<br />
** Enhanced the workflow for creating text annotations. This approach should serve as a general framework for all annotations (sequence diagram available http://wiki.na-mic.org/Wiki/index.php/File:TextAnnotationWorkflow.png)<br />
** modified vtkMRMLInteractionNode to support the place modes for the annotations<br />
*** meet with Wendy next week to discuss integration<br />
** added a click counter class to support the creation of widgets with multiple clicks (very generalized to support all annotations)<br />
*** plan is to place seeds before the actual widget gets created<br />
* 07/29/10<br />
** Created an extra layer called vtkMRMLAnnotationDisplayableManager which serves as a superclass for all specific Annotation displayableManagers. F.e. the vtkMRMLAnnotationTextDisplayableManager is now really lightweight.<br />
** Coordinated with Wendy to add additions interaction modes to vtkMRMLInteractionNode to support different interaction types for different annotations. This will happen under the hood, so the user sees only the "place" mode.<br />
** Got together with members of the 3D & Advanced Imaging Lab at UPENN to investigate how commercial products realize annotations (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:vtkWidgets#How_do_they_do_it.3F).<br />
** Interactive placement of text annotations is now possible. This should be the standard way of placing annotations for all available types.<br />
** Added a test for the creation of a text annotation and its widget without a displayableManager (vtkMRMLAnnotationTextNodeAndWidgetTest1)<br />
** Removed initial values from AnnotationNodes due to different seg-fault errors when properties where not initialized. To cut down confusion, no initializations are now necessary.<br />
* 07/22/10 <br />
** Meeting of Nicole, Steve and Daniel to talk about architecture<br />
*** biggest change is the introduction of a hierarchy for annotation<br />
**** more information and discussion during the tcon:[[Projects:ARRA:miAnnotation_Meeting_07202010|Meeting / Weekly meeting]]<br />
** fixed AnnotationTextDisplayableManager to support multiple text annotations<br />
** added a test for the AnnotationTextDisplayableManager<br />
** property dialog for annotations gets displayed again, nevertheless the connection to the MRML display nodes needs further work<br />
* 07/15/10<br />
** add text nodes using the new displayable manager architecture is now possible<br />
*** nevertheless, full functionality is not restored yet<br />
** added fiducial displayable manager<br />
** new Slicer bug tracker category: Annotations<br />
*** filed open bugs and feature requests - please add all new requests there<br />
* 07/08/10<br />
** moved tests to Testing/Cxx<br />
** created a superclass for all displayable managers (vtkMRMLAnnotationDisplayableManager)<br />
** created vtkMRMLAnnotationTextDisplayableManager based on the old qMRMLAnnotationTextManager<br />
** working on the add text node functionality with the new displayable manager<br />
** fixed linking errors appearing on the Slicer Dashboard<br />
* 07/01/10<br />
** re-factored module from miAnnotation to Annotation<br />
** re-integrating functionality without KWWidgets<br />
*** MRMLDisplayableManager was created by Kitware guys and includes base functionality for the re-integration<br />
*** starting with adding text nodes<br />
**** UML diagram for involved classes: [[MiAnnotation_Documentation#Development]] (needs to be checked for logic/manager/mrml pattern consistency) <br />
** added option to set helptext for the module in consistency with qSlicerWidget<br />
* 06/24/10<br />
** Compiling without KWWidgets on Mac OS is now possible.<br />
** Starting to include the functionality of KWWidgets in pure QT code.<br />
** Daniel Haehn took over project from Yong Zhang.<br />
* 06/18/10<br />
** Tutorial is created.<br />
** GetAnnotationMeasurement is modified to return multiple measurements.<br />
** ROI annotation is modified to display extension measurements.<br />
** Bidimensional annotation is modified to display bi-line measurements.<br />
* 06/11/10<br />
** Documentation page is created.<br />
** Bugs for property dialog are fixed.<br />
** Constructions of Bidimensional and Spline annotations are modified using proper control point initialization.<br />
** Bugs for showing values for some annotation types are fixed. <br />
* 06/04/10<br />
** vtkSlicerAnnotationROIManager is implemented.<br />
** vtkSlicerAnnotationTextManager is implemented.<br />
** vtkSlicerAnnotationSplineManager is implemented.<br />
** vtkSlicerAnnotationBidimensionalManager is implemented.<br />
* 05/28/10<br />
** vtkMRMLAnnotationROINode is added;<br />
** vtkMRMLAnnotationBiDimensionalNode is added;<br />
** vtkMRMLAnnotationSplineNode is added.<br />
** Logic and ModuleWidget are modified to include new Nodes<br />
* 05/21/10<br />
** ROI, Text, BiDimensional, and Spline Annotations are initialized.<br />
** fixed BUG: HTML report cannot be saved properly.<br />
* 05/14/10<br />
** fixed BUG: When opening display properties from Sticky note -> reduce frame and enlarge it again by pressing triangle next to title : value and coordinates appear<br />
** fixed BUG: fiducial manager is added.<br />
** fixed BUG: AnnotationMouseModePick/Place are updated.<br />
* 05/07/10<br />
** fixed BUG: Lock does not lock the position of a widget in the 3D Viewer<br />
** fixed BUG: changing coordinates to AngleNode does not have any effects on the Angle Widget.<br />
** fixed BUG: fix coloring for annotation selection<br />
*04/30/10<br />
** fixed BUG: changing control points cannot be done when property dialog is open.<br />
** fixed BUG: annotation is not highlighted when selected.<br />
** fixed BUG: starting from the 2nd annotation, changing the location of the left point for ruler or center point for angle does not update the table properly.<br />
** fixed Bug : changing the center point of angle node does not update table properly<br />
* 04/23/10<br />
** Created a ruler widget manager <br />
* 04/16/10<br />
** Created the new annotation type sticky note, which allows you to enter text independent from the viewer<br />
* 04/09/10<br />
** Modified source code to be compliant with VTK 5.6<br />
** Grid out your buttons (Create Frame)<br />
** Fixed BUG: When changing line color in Display Properties it changes the Text Color<br />
** Added script for testing color setting <br />
** Fixed BUG: Label of line color changes in property window when defining a unselected color<br />
<br />
* 04/02/10<br />
** Fixed BUG: Nothing happens when Property Window is open and you press the edit button for another annotation<br />
** Restructured Annotation MRML<br />
** Fixed Bug: Resetting of Lines and Points does not work correctly GetNumberOfLines > 0 <br />
<br />
* 03/26/10<br />
** The property restoration is now implemented properly.<br />
** Property Modification is re-designed to simplify the operation.<br />
** Removed bug: ruler/angle disappear after adding fiducials <br />
** Removed BUG: in property dialog, when editing the text, the character is entered from right to left.<br />
** include lock annotation into option button (use same logic as for new (De)select All button)<br />
** For each annotation type provide list outlining which display property can be changed, which cannot , and which one you do not know <br />
** Resolved BUG: When saving a report with a file name that already exists then the following message appears in the command shell "Error: cannot make directory" and directory with files is not updated<br />
** Resolved BUG: Annotation Properties: (Un)selected color is initially white even though widget in 3D viewer is different<br />
** Resolved BUG: Select Color window does not show the correct color<br />
** Resolved BUG: Selected and Unselected Color are switched<br />
** Define Tooltips for fiducial, angle, ruler,report, save mrml button<br />
** In table: Add proper tool tip for visualization and edit button<br />
** Resolved BUG: when saving report with out ending html to the file name - icons will not be saved under Linux<br />
** Created Test Module for testing miAnnotation logic<br />
** In collaboration with Nicole Aucoin figured out line display bug in 3D Viewer <br />
** Use the Kitware slider and colorPicker under Display Property<br />
** Fixed BUG: Slicer crashes when creating an annotation while Display properties is open, and when closing the property window and then pressing edit for the new annotation<br />
<br />
* 03/19/10<br />
** In the property window display properties are shown via collapsed frame by default<br />
** List all attributes for text/point/line and implement those that can be modified<br />
** Fixed BUG: When pressing the property button warning messages pop up in my command shell <br />
** Annotation Properties: For Angle and Ruler Widget also shows now values of AnnotationDisplayNode and AnnotationControlPointsNode<br />
** Change design of html report <br />
** Implemented text edition and update for ruler and angle widgets.<br />
** Changed the default mouse mode icon to MousePick.<br />
** Modified Report Dialog to avoid horizontal slider when screen shot is included in the report.<br />
** Removed multiple warning messages.<br />
** Fixed Bug in Report: empty text fields are displayed without boundaries <br />
** Ruler Distance is now displayed just in mm <br />
** After talking to BWH changed name of tool from Reporting to miAnnotation<br />
* 03/12/10<br />
** Created icons for:<br />
*** edit conditioning for all annotation types (done), <br />
*** mouse mode icons, pause, play, cancel, ok/done, (Un)lock (done)<br />
*** new the annotation types poly line, spline with control points, volume information extractor, and sticky note (done)<br />
*** Modify fiducial icon just to show one star and change save annotation icon (done)<br />
*** Modify save annotation and save scene icons (done)<br />
*** Modify move up/down delete icons (done)<br />
** Write 5 page, double column, AMIA paper about Reporting<br />
* 03/05/10<br />
** Removed Warning Messages when compiling<br />
** Fixed Bug: When entering text in property box (under linux) it is entered from right to left instead left to right <br />
** Fixed Bug: Annotation Property: funny behavior with selecting set of digits in a numerical value and typing in a numeric value - only the first digit gets change.<br />
** Fixed Bug: Value of Angle node is not update in table<br />
** Fixed Bug: Updating the value in the table slows down the operations<br />
** Changed the default ruler from 1mm to 500mm.<br />
** Angle Widget is added by manually clicking three points on the viewer. The angle value is now shown in the table. The behavior of the angle button is in the "toggle down" state until all three control points are set<br />
** When selecting annotation in table, color of annotation in 3D Viewer changes to selected color <br />
** Revised "add ruler" button to click-style instead of toggle-style<br />
** When creating a new annotation, set this entry to selected and all other table entries to unselected<br />
** (De) Select All button: change as discussed with Wendy Plesniak, BWH, to option button with proper logic<br />
** Setting color/selected color for individual Ruler and Angle widgets in property dialog<br />
** Fixed Bug: hiding/unhiding ruler and angle annotations<br />
** Change display property for each annotation individually<br />
** Lots of warning messages when compiling code<br />
* 02/26/10<br />
** Created pop up window showing screen shot<br />
** Manual editing of coordinates via "Property Window"<br />
** Resolved column width problem in table ([http://wiki.na-mic.org/Wiki/index.php/File:Screenshot-Form.JPG original problem], [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_TableV2.png second screen shot problem])<br />
** Fixed bug where hide icon changed size in table<br />
** Include icons when saving html report in a directory with the same name as the html file<br />
** [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_GUI.png Reorganized GUI] based on feedback from Wendy Plesniak, BWH <br />
** Include screen shots (if any) in the report (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_ReportV1.png an example])<br />
** Fixed the following bug: After resizing the 3D Window taking a screen shot only displays the window with the original size (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Window.png screen shot]) <br />
** Fixed Bug: Value update of ruler widget is slow <br />
** Text defined in property box now shows up in table<br />
** Integrated vtkMRMLAnnotationAngleNode with AngleWidget<br />
** Added new buttons to create frame based on feedback from BWH <br />
* 02/19/10 <br />
** Implement a general structure for vtkMRMLAnnotation*Node<br />
** Work together with Kitware to resolve QT Table layout problem <br />
** Allow defining long text annotations for each widget<br />
** Improve user interaction through pop up windows when trying to modify an existing annotation <br />
** Creating and removing ruler now works correctly <br />
** Use correct label format to display measurement values in Annotation Property window <br />
** Created a "Save annotation" Window<br />
** Fixed changing icon size in table (see original [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Table-IconProblem.png screen shot] )<br />
** Fixed slicer crashing closing the property window <br />
** Renamed and resized columns in Table<br />
*02/12/10 removed bugs related to table buttons, linked button to angle widget and ruler widget<br />
*02/05/10 implemented "Save Annotation Report" button and "Move up/down" buttons; added extra column in the report table for visibility; modified annotation property dialog; implemented button-click in the table.<br />
*01/29/10 implemented functionality for "Annotation Property Modification" button, "Create Report" button, and integrated new icons for buttons.<br />
*01/22/10 Set up the source control for the reporting module; implemented functionality for "Select All" button, "Visible" button, and "Delete" button in the GUI; created new icons for buttons<br />
*01/15/10 Organized biweekly Tcon <br />
*01/08/10 Participated in all week All Hands Meeting in Utah; Expanded QT interface with functionality to set seeds in images; Defined a final MRML Structure for storing annotation. <br />
*01/01/10 Generated a [[Media:SlicerAM QtAnnotation.png | GUI interface]] via QT for the annotation module. [[Projects:ARRA:SlicerAM#Widget_related_action_items | Reviewed ]] all VTK Widgets related to annotation. <br />
*12/25/09 Created [[ 2010_Winter_Project_Week_mComment | project ]] and organized [[ AHM2010:AnnotationBreakout | break out session ]] at AHM meeting. Coordinated efforts with BWH team in preparation of the meeting. <br />
*12/18/09 Held workshop to integrate AMI into 3D Slicer. Hired new person to implement AMI in Slicer. <br />
*12/11/09 [[ Projects:ARRA:SlicerAM_RSNA09Report | Summary ]] of tools demoed at RSNA <br />
*12/04/09 Visited RSNA to review annotation tools by GE, Siemens & Phillips. Connected to caBIG AIM project to see how we can make use of their data scheme <br />
*11/29/09 Created GUI for MarkUp module <br />
*11/20/09 Design MRML Structure of Annotation and MarkUp Module<br />
*11/13/09 Organize [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]] Session<br />
*11/06/09 Designed User Interface , Meet with Julien Finet and Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Participated in Qt-Tcon, Interviewed candidate at Almaden, coordinated efforts with Nicole Aucoin <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<br />
<br />
= Feature Request =<br />
== VTK Widgets ==<br />
* For further detail go [[ Projects:ARRA:SlicerAM:KWWidgets | here ]]<br />
<br />
== QT Related ==<br />
* Submit bugs and feature request via [http://na-mic.org/Mantis/search.php?project_id=1&category=QtGUI&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 Mantis]<br />
* Feature requests that may open discussions can be added [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/OpenDiscussions here]<br />
<br />
== Daniel ==<br />
All features/issues are listed here: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
=== Known issues ===<br />
* MRML<br />
** <strike>After loading of scene, the annotations are not displayed in the hierarchy tree anymore</strike><br />
** Load scene does not display 3D widgets, Import scene does<br />
** After importing or load, the user has to click on the widget to enable the connection between tree entry and widget<br />
* Annotations<br />
** Property dialog does not work yet and might crash<br />
** Pick mode does not work correctly, if placement was paused and resumed (the first picked coordinate gets lost)<br />
** <strike>Screenshot imagedata does not get saved on Scene save</strike><br />
* GUI<br />
** if moving an annotation up or down inside a hierarchy, the tree gets confused<br />
** Drag and drop does not work<br />
** <strike>after creating hierarchies, the selected item does not reflect the hierarchy which new annotations get added to</strike><br />
** save buttons not implemented<br />
** <strike>widget intersections do not work</strike><br />
** <strike>Slicer4 crashes on exit after annotations were placed and the scene was not closed manually prior exiting Slicer</strike><br />
<br />
==== Feedback by Users ====<br />
* Ron<br />
<pre><br />
1. I sometime like the fiducials to be spheres, not crosses. In Slicer 3 we had a whole list of options. Can I have them for Slicer4? Can I also change their size?<br />
2. The ruler has different colors in the 3D view and in the slice views. That is wrong.<br />
3. The properties popup require a lot of clicking, including double click. Usability will need to be optimized.<br />
4. No drag and drop in the module.<br />
5. text annotation: arrow in the slice view, but not in the 3d view (see attached)<br />
6. text is not in the box in the slice view<br />
7. the font is butt-ugly. In addition, part of the letter n is cut off by the t. The space between the capital V and the e is too big<br />
8. Slicer 3 let you jump to a fiducial location by right clicking in the list in the module.<br />
9. Also, The ruler does have issues with visibility, when the slice is rendered as well. See attached screensnapshot: little dots to the left, no dots to the right.<br />
</pre><br />
* Isaiah<br />
<pre><br />
1) need "selected" parameter for each fiducial, separate from visibility. It's used as boolean inclusion criteria in several modules - in my case DTI FiducialSeeding but also some other ones like segmentation and for CLI modules.<br />
2) need to set properties for groups of fiducials at once. This is tricky because the hierarchy is generic, but ability to set all parameters for a group of fiducials in one place is important.<br />
3) meta visibility control is helpful but maybe not imperative, ie show/hide a whole group but still maintain the individual visibility settings.<br />
4) flicker of fiducials in 2d-view slice whenever other fiducial is moved across that slice. I have two coplanar fiducials in coronal slice, and move a third back/forth across the axial slice. Each time the third crosses the coronal there is a noticeable flicker of the two fiducials in-plane.<br />
5) positioning with decimal precision rather than integer?<br />
6) the persistent-drag mouse interaction in both 2d and 3d is not ideal (at least to me).<br />
7) deleting a hierarchy with ~30 fiducials incurs a noticeable delay around 7s. I compiled with the standard (debug mode?) instructions on x86, ubuntu 10.04.<br />
8) there are some strange mouse interactions when placing in the 3d view after clicking the "cancel" or "accept" buttons. for example, the first time I create a list it works fine: one click to place each. However, if I stop, delete, and start adding again then it doesn't work the same way: the first click makes a fiducial, but subsequent clicks only occasionally place new fidus. I think the problem is that the interactor is selecting the new first fiducial even if the mouse is very far away - can click on the other side of the screen and drag that fiducial, even after pressing "stop" again.<br />
8a) minor style: is it possible to use stop-sign or something else rather than the current x-in-circle for "cancel"?... my brain sees that as the fiducial button 1/2 the time :)<br />
9) I'm confused by the edit properties display (window) for fiducials. What is the purpose for each tab: text, points, lines? points seems to be a place for a list, but x/y/z is empty and position is instead displayed under "Measurement value" on the text tab.<br />
</pre><br />
<br />
==== Meeting with Ron 05/06/11 ====<br />
Nicole and Daniel met with Ron to discuss usability issues and future development.<br />
<br />
<br />
* <strike>Ron would like the 3d sphere to be the default setting for the glyphs.</strike> (H)<br />
* Change the mouse cursor when in place mode, use the images from the mouse modes toolbar icons. (H)<br />
* Text annotations <br />
** line breaks for long text, automatic (H)<br />
** show some of the text (first 20chars?) in the fiducial text box with ... to denote more visible in the Qt interface (M)<br />
** sometimes don't want an arrow head (M)<br />
** consolidate the text and fiducials into one conceptual package allowing turning on/off the text box, detaching it, leader, etc. (L)<br />
** get the text working in 2d slice windows (H)<br />
* Set one time place as the default in the annotation module (add a persistent radio button?) (H)<br />
* Rulers <br />
** expose the tick mark options in the GUI (need to support mice, humans, galaxies) (L)<br />
** use the NeuroDTI example data set from Ron's drop box (H)<br />
** 3d tumor model when measuring it's diameter, the measurement text is hidden inside of it, add an option to position the text at and end or in the middle (H)<br />
** toggle label visibility (M)<br />
* Bidim <br />
** does RECIST need to be orthogonal? Yes<br />
** add the word orthogonal to the tooltip (done)<br />
** make a new icon with a quarter circle between two arms of the axes and use it (L)<br />
* Reformat widget <br />
** estimated time to implementation? (email sent to Will S.) <br />
* Save <br />
** <strike>Ron vetoed the Save panel in the Annotation module, all saving is to be done via the centralised widget (H)</strike><br />
** <strike>take out the save/load buttons, move the report buttons to another part of the GUI (H)</strike><br />
** add the screen snapshot functionality (especially the over sampling) to the scene views pop up window and bring it up from the shortcut box in the lower left of the GUI (this may need some infrastructure changes) (H)<br />
* Workflows <br />
** use the DTI Tumor scene as a sample (M)<br />
** when Ron created the views, each scene view is a workflow end point <br />
** once the annotation functionality is all there, Nicole will meet with Ron and add the annotations to the scene view and save a new scene, and also document the process for usability improvements and testing (M)<br />
* ROIs<br />
** see the Slicer3 crop volume module for a good initialization method: make the ROI node and then update it by clicking in the 2d slice (M)<br />
** 2d annotation ROI -> label map (H)<br />
** match handle colours of the widget to 2d elements in the GUI (H)<br />
** implement the fit ROI to volume functionality (L)<br />
*** once it is included in volume rendering in Slicer 4 please take a look at this functionality - if it is easy to import than it has high priority <br />
* Scene views (M)<br />
** test the Neuro DTI file on Slicer4 <br />
** create a new Slicer4 Annotation Testing mrml file and upload it to the drop box<br />
<br />
= Display Properties of Widgets =<br />
* Unavailable / Unknown:<br />
** Set text colors for Ruler and Angle Widget <br />
** Get/Set glyph scale / point size for point display node<br />
** Get/Set text opacity/ambient/diffuse/specular from text display node <br />
** Color of "angle line" cannot be defined <br />
* Available:<br />
** Get/Set text colors from display node<br />
** Get/Set text scale from display node<br />
** Get/Set point colors from point display node<br />
** Get/Set point opacity/ambient/diffuse/specular from point display node<br />
** Get/Set line colors from line display node<br />
** Get/Set line width/opacity/ambient/diffuse/specular from line display node<br />
** Get text format for angle and ruler</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation&diff=67140Projects:ARRA:miAnnotation2011-05-13T15:42:34Z<p>Pohl: /* Meeting with Ron 05/06/11 */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
<br />
= Aim =<br />
[[Image:SlicerAM_QtAnnotation.png|241px|right|Annotation Module]]<br />
<br />
Medical images often contain a wealth of information, such as anatomy and pathology, not explicitly accessible. One way to address this issue is via image annotation and markup. We propose to create a comprehensive framework for annotation and markup within 3D Slicer, enabling users to capture structured information easily. Furthermore, we will develop schemas for saving and recovering this information into and from XNAT, allowing queries of larger data sets of medical scans. This tool will provide clinicians with a relatively simple way to capture information latent in medical scans, and also to select micro-cohorts of medical scans for studying diseases.<br />
<br />
= Research Plan =<br />
3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include: <br />
* a rich set of geometric objects for improved visual differentiation between annotations<br />
* markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection<br />
* entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologiesand <br />
* a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT.<br />
<br />
We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region.<br />
<br />
The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values. <br />
<br />
Both modules are accompanied by training materials and documentation to ensure usability.<br />
=Design of Module=<br />
* Current [[Media:AMI-GUI-Design.ppt | GUI ]] outline - [[Media:SlicerAM QtAnnotation.png | Screenhot]] in Slicer <br />
* Suggested [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] outline<br />
* Wendy's Mouse Mode sketches http://www.slicer.org/slicerWiki/index.php/Slicer4:UIDesign:MouseModeSketches<br />
<br />
= Documentation=<br />
* [[ miAnnotation_Documentation | Documentation ]] of the module<br />
* Using the [[Media:Slicer4_miAnnotation.ppt | module]] with corresponding data ([[Media:Slicer4_miAnnotation_data.zip | sample data]] )<br />
<br />
=Key Personnel=<br />
10% Kilian Pohl (UPenn) <BR><br />
95% Daniel Haehn (UPenn) <BR><br />
5% Dominique Belhachemi (UPenn) <BR><br />
<br />
=Past Contributors=<br />
Yong Zhang (IBM) <br><br />
<br />
=Events=<br />
* 05/18/10 [[Media:miAnnotation_May2010_Yong.pdf | Presentation]] at the Department of Healthcare Informatics, IBM, Almaden<br />
* 12/16/09 - 12/17/09 [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]]<br />
* 01/06/10 [[AHM2010:AnnotationBreakout | Break out session]] at AHM 2010<br />
* 01/19/10 Biweekly Annotation Tcon from 4:00 - 5:00 pm EST (next meeting 2/9): Tel: (218) 862-1115 Conference ID: 348265#, [https://www.lotuslive.com/join?schedid=4572317 Desktop Sharing ]<br />
* 08/30/10 Budget Year 1 [[ Projects:ARRA:SlicerAM:Meeting20100831 | Review meeting ]]<br />
<br />
=Progress=<br />
* 13/05/11<br />
** MRML: add required modified events for certain display properties<br />
** add opacity slider to text properties in the property dialog<br />
** add a spacer to the property dialog to have a consistent design for text, point and line properties<br />
** add label position to the display node<br />
** add utility methods to get the text, point, line display nodes for a given mrml node id<br />
** handle the main annotation types when setting them active in the selection node<br />
** hook up the text opacity, the point material properties. Grey out the line tab if no line display node. Add the point values to the table in the points tab<br />
** removed the Save panel from the module GUI and moved the buttons for report and screenshot in the edit toolbar (this might change at one point)<br />
** added a storage node for the annotation screen snapshot node to properly save the screenshots<br />
** cleanup of annotation snapshot nodes<br />
** use the text opacity, the point material properties<br />
** add value constraints for several sliders in the property dialog<br />
** MRML: add new method SetControlPoint(id, coords) without the visible and selected flags<br />
** property dialog now complete for text, point, line! (not for hierarchies yet)<br />
* 06/05/11<br />
** fiducials are now shown the same way in 2D and 3D<br />
** the property dialog is connected to configure point colors and glyph types for fiducials<br />
** it is possible to add text to a fiducial in 3D<br />
** meeting with Ron to discuss further development and usability issues<br />
* 04/29/11<br />
** fixed the flickering when placing or interacting with fiducials and rulers<br />
** removed some obsolete render calls to enhance performance<br />
* 04/22/11<br />
** worked together with Nicole<br />
*** finally fixed the crash on Slicer exit<br />
*** investigated why MRMLScene import works fine with the annotations but MRMLScene load does not<br />
**** first success: import and load mrml scenes now both load the annotations in 2D and 3D<br />
* 04/15/11<br />
** Maintenance<br />
* 04/08/11<br />
** Maintenance<br />
* 04/01/11<br />
** Maintenance<br />
* 03/25/11<br />
** Maintenance<br />
* 03/18/11<br />
** Work on MRML Load/Save issues (Nicole)<br />
** Maintenance<br />
* 03/11/11<br />
** Work on hierarchies (Nicole)<br />
** Maintenance<br />
* 03/04/11<br />
** Maintenance<br />
* 02/25/11<br />
** Maintenance<br />
* 02/18/11<br />
** Maintenance<br />
** Communication with Daniel Rubin from Stanford to plan AIM integration<br />
*** provided Annotation MRML examples<br />
* 02/11/11<br />
** Maintenance<br />
* 02/04/11<br />
** Clarified how to add Node Selectors for Annotations to the GUI of 3rd Party 3D Slicer Modules<br />
*** Kitware provided necessary infrastructure<br />
*** Proof of Concept in the new CropVolume module with ROI Annotations (Andriy)<br />
** Clearing up the Annotation Storage Node Tests (Nicole)<br />
* 01/28/11<br />
** Presented Annotation module and SceneView module at NAC EAB Meeting<br />
** Smaller bugs and maintenance<br />
** Meeting with Nicole and Alex concerning the final API of hierarchies in Slicer4<br />
* 01/21/11<br />
** Re-activated ROI annotation with backwards compatibility to the old vtkMRMLROINode<br />
*** Tested successfully with a scene from Slicer3<br />
*** Provided documentation to relevant people<br />
** Rulers now support the measurement tape behavior<br />
** Changed the UPenn logo<br />
** Several smaller fixes<br />
** provided Wendy with Screenshots for NAC Poster<br />
*** [[File:Annotation.png|none|thumb|The current state of the Annotation module.]]<br />
*** [[File:Report.png|none|thumb|The report dialog.]]<br />
** Found displayableManager inconsistency between 2D and 3D and the MRML Node Added Event<br />
** MRML backwards compatibility fix for all Annotations<br />
*** new tag "visible", old tag "visibility"<br />
* 01/14/11<br />
** Attended NA-MIC project week<br />
**Enabled picking when placing annotations in 3D. <br />
**Fixed display of ruler intersections. <br />
**Added new icons. <br />
**Use only three seeds to place bidimensional widgets which results in more stability. <br />
**It is also now possible to add annotations to the toplevel hierarchy after another hierarchy was created by clicking in an empty space of the treeView.<br />
**Re-added the ROI functionality, so now we have 5 widgets<br />
**Ruler: enabled display of ticks (measuring tape mode) in 2D and 3D<br />
* 01/07/11<br />
** re-factored the annotation module in terms of changes in the Slicer4 environment<br />
*** ready for the new developer release<br />
** worked on the outsourced SceneView functionality to make SceneViews survive round-trips (mrml load and save)<br />
* 12/31/10<br />
** Maintenance<br />
** Documentation<br />
* 12/24/10<br />
** Maintenance<br />
** Received the first bug reports of potential users<br />
*** Updated bugtracker<br />
* 12/17/10<br />
** Extended Report functionality<br />
*** now includes screenshots<br />
*** shows the hierarchies<br />
** Sorting of Annotations now possible<br />
** Widgets:<br />
*** added the 3D representation of rulers<br />
*** removed the vtkInteractorRecorder hack by placing the widgets programmatically<br />
** Outsourced the former integrated scene snapshot functionality<br />
*** Wrote a new module called SceneViews<br />
*** vtkMRMLSceneViewNode replaces the old snapshot node and includes thumbnail, description..<br />
**** is not part of the displayable framework anymore<br />
** Added confirmation questions prior to removing annotations<br />
** Worked on MRML save/load<br />
** Updated the priority list: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
** Added a section for known issues: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation#Known_issues<br />
** Annotation module Lines of Code (without .ui files and no blank lines): 24820<br />
* 12/10/10<br />
** Changed some things in the MRML architecture to enhance encapsulation<br />
*** Adding new Annotations should be easier now<br />
** Lock selected, toggle visibility of selected and delete selected implemented<br />
** Report functionality works again<br />
*** Added support to print and export as a HTML report<br />
* 12/03/10<br />
** Added icons to the hierarchy tree<br />
** Configured a proxy model to display only vtkMRMLAnnotationHierarchyNodes and vtkMRMLAnnotationNodes in the hierarchy tree<br />
** Smaller layout fixes<br />
** Added 'full layout' thumbnail functionality to Annotation snapshots<br />
** Removed the old table and replaced fully by the treeView<br />
** Over 1000 of lines of code were removed<br />
*** Hierarchies are now usable<br />
*** [[File:Annotationscreenshot.png|none|thumb|Screenshot of an example Annotation using the new features]]<br />
* 11/26/10<br />
** Added functionality to the module logic to be able to place fiducials programmatically<br />
*** This will be used if one presses the 'p' key on a slice view<br />
** Re-activated the text annotation<br />
*** Used vtkCaptionWidget instead vtkTextWidget to be able to have an anchorpoint in 3D space<br />
** The scene, camera and view nodes are now hidden from the hierarchy tree<br />
*** The toplevel annotation hierarchy is the new root and also hidden<br />
** Added functionality to show Annotation snapshot nodes in the hierarchy tree<br />
*** This required adding the original snapshot node to the displayable framework (as a workaround)<br />
*** Later, we will add thumbnail and description directly to vtkMRMLNode, so that a screenshot can be attached to every MRML node<br />
** Overall code polishing in terms of code conventions<br />
*** including the destruction of the frozen seedWidget on Slicer exit<br />
* 11/19/10<br />
** Small fixes to the Annotation snapshot functionality<br />
** New functionality: reset view to when the annotation was placed<br />
** Derived qMRMLAnnotationTreeWidget and qMRMLSceneAnnotationModel to support hierarchies in the module<br />
*** the widgets let us customize the look and feel of the treeWidget<br />
*** in this context, fixed the creation of hierarchies to a specific order in the scene (which is need for the widget)<br />
*** the Annotation hierarchy nodes and the Annotations get already displayed in the treeWidget<br />
** Fixed stack smashing in connection with a recently introduced compiler flag<br />
* 11/12/10<br />
** All widgets are now restricted to the current renderer which makes the interaction more robust.<br />
** Fixed funky behavior after fiducials were placed.<br />
** New functionality: Annotation snapshots (screenshot + description + scene snapshot) implemented.<br />
*** [[File:snapshot1.png|none|thumb|The new annotation snapshot functionality (part 1)]] [[File:snapshot2.png|none|thumb|The new annotation snapshot functionality (part 2)]]<br />
* 11/05/10<br />
** Widget Design Fiesta http://www.na-mic.org/Wiki/index.php/WidgetDesign2010<br />
** Widget intersections works nearly perfectly<br />
*** Unfortunately, only for centered datasets<br />
** Restrict ruler placement to the current renderer works now. This means, the ruler does not disappear when one point moves outside the sliceview.<br />
* 10/29/10<br />
** Lightbox view works for Fiducials<br />
*** Other widgets have to be refined to be used in a lightbox view due to inconsistent VTK API. The VTK Widget Fiesta should target this.<br />
** Widget intersections in the works, not perfectly working yet.<br />
* 10/22/10<br />
** Priority list for the December release of Slicer4: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
* 10/15/10<br />
** Adopting the old TCL logic to enable 2D widgets on reformats and lightbox views<br />
*** Still working on the lightbox view (very close)<br />
* 10/08/10<br />
** Code-cleanup of the logic class - any old and clumsy code was removed.<br />
** Introducing the StringHolder design pattern [(c) Steve] to always show measurement correctly in the GUI.<br />
** Widget creation now works on Unix aswell.<br />
** Added the RegisterNodes method to register node classes when the scene gets attached to the logic class.<br />
** Hierarchy nodes get added when an annotation is created (code workflow to be optimized).<br />
** Configured a nightly build system to build and test the annotation code every night on a SPL workstation.<br />
* 10/01/10<br />
** The hierarchy changes will replace the table in the GUI with a tree widget<br />
*** Added a tree widget to the GUI additionally to the table to display both during the transition stage<br />
** Fixed the follower bug, which sometimes dragged the second controlpoint of a widget behind when the other controlpoint was moved.<br />
* 9/24/10<br />
** Wrote performance test for vtkWidgets in a standalone VTK mode<br />
*** compared performance in Slicer against standalone VTK<br />
*** rendering of text labels was found to be the performance hog, disabling these labels increases performance inside and outside Slicer dramatically<br />
** Meeting between Wendy, Nicole, Steve and Daniel to review the Annotation module status<br />
*** Notes: [[Projects:ARRA:SlicerAM:Meeting20100921]]<br />
** Annotation hierarchy in the works<br />
* 9/17/10<br />
** 2D placement of Rulers, Bidimensional and Fiducials works now<br />
*** The widgets get synchronized along the slice viewers and the 3D view<br />
** Added extra layer on top of vtkWidgets and vtkWidgetRepresentations to add some extra functionality like calculating distances of measurement correctly in 2D<br />
*** bidimensional measurement and rulers now show the correct distance also in 2D<br />
** Fixed possible null pointer exception in vtkMRMLSliceLogic<br />
** Refactored GetSliceOffSet from vtkMRMLSliceLogic to vtkMRMLSliceNode<br />
* 9/10/10<br />
** 2D placement of Annotations in the works<br />
*** change of the underlying architecture to use one displayableManager for 2D and 3D resulting in less code duplication<br />
*** to perform the changes, all annotations but fiducials were disabled for now<br />
* 9/3/10<br />
** Annotation module status review and planning meeting took place in 1249 Boylston<br />
*** Agenda and Notes: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:Meeting20100831<br />
**** includes new generated class diagram<br />
** Property dialog updated (see screenshot)<br />
*** [[File:Annotationpropertydialog.png|none|thumb|The new annotation property dialog.]]<br />
*** first MRML-Widget synchronization works, the text tab in the property dialog works well with the text widget<br />
** new icons for bidimensional measurement and ROI by Wendy<br />
** updated ctkColorPickerButton to include the ability to disable the setting of the color hexcode as the buttontext to avoid the workaround we had in the annotation module<br />
* 08/27/10<br />
** added a work-around to initialize renderer properly resulting in improved display of annotations in 3D viewer<br />
** cleaned up the code (more then 1000 lines of code where obsolete)<br />
** updating property dialog, which includes revisiting the displayableManagers to support MRML and widget updates<br />
* 08/20/10<br />
** fiducials and sticky node work now<br />
** ruler and spline work now<br />
*** spline widget causes problems b/c after one spline was placed, no interaction with 3D scene possible<br />
** ROI works now<br />
** all annotations now can be placed to examine widget behavior<br />
** started working on a new interface for the property dialog<br />
** consolidated experts for 2D slice displayableManagers<br />
** started working on synchronizing the widgets with MRML display nodes<br />
** fixed GUI problem: the table did not expand even if there was free space in the module frame. now it works.<br />
* 08/13/10<br />
** Wendy, Nicole and Daniel discussed how to integrate mouse modes of Slicer into Annotation module and vice versa. Solution is a widget which appears in the Annotation module panel but can also be shown outside of it as a toplevel window in Slicer (maybe with keybinding), see here: http://wiki.na-mic.org/Wiki/index.php/File:Widget.png<br />
** current status (workflow, user places seeds and widget appears):<br />
*** angle annotations work (note: the widget did not support programmatical placement. a trick is used to place the widget where the user has clicked)<br />
*** text annotations work<br />
** modified vtkMRMLInteractionNode to have a customTag for place modes not only from annotation module but all modules<br />
* 08/06/10<br />
** Enhanced the workflow for creating text annotations. This approach should serve as a general framework for all annotations (sequence diagram available http://wiki.na-mic.org/Wiki/index.php/File:TextAnnotationWorkflow.png)<br />
** modified vtkMRMLInteractionNode to support the place modes for the annotations<br />
*** meet with Wendy next week to discuss integration<br />
** added a click counter class to support the creation of widgets with multiple clicks (very generalized to support all annotations)<br />
*** plan is to place seeds before the actual widget gets created<br />
* 07/29/10<br />
** Created an extra layer called vtkMRMLAnnotationDisplayableManager which serves as a superclass for all specific Annotation displayableManagers. F.e. the vtkMRMLAnnotationTextDisplayableManager is now really lightweight.<br />
** Coordinated with Wendy to add additions interaction modes to vtkMRMLInteractionNode to support different interaction types for different annotations. This will happen under the hood, so the user sees only the "place" mode.<br />
** Got together with members of the 3D & Advanced Imaging Lab at UPENN to investigate how commercial products realize annotations (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:vtkWidgets#How_do_they_do_it.3F).<br />
** Interactive placement of text annotations is now possible. This should be the standard way of placing annotations for all available types.<br />
** Added a test for the creation of a text annotation and its widget without a displayableManager (vtkMRMLAnnotationTextNodeAndWidgetTest1)<br />
** Removed initial values from AnnotationNodes due to different seg-fault errors when properties where not initialized. To cut down confusion, no initializations are now necessary.<br />
* 07/22/10 <br />
** Meeting of Nicole, Steve and Daniel to talk about architecture<br />
*** biggest change is the introduction of a hierarchy for annotation<br />
**** more information and discussion during the tcon:[[Projects:ARRA:miAnnotation_Meeting_07202010|Meeting / Weekly meeting]]<br />
** fixed AnnotationTextDisplayableManager to support multiple text annotations<br />
** added a test for the AnnotationTextDisplayableManager<br />
** property dialog for annotations gets displayed again, nevertheless the connection to the MRML display nodes needs further work<br />
* 07/15/10<br />
** add text nodes using the new displayable manager architecture is now possible<br />
*** nevertheless, full functionality is not restored yet<br />
** added fiducial displayable manager<br />
** new Slicer bug tracker category: Annotations<br />
*** filed open bugs and feature requests - please add all new requests there<br />
* 07/08/10<br />
** moved tests to Testing/Cxx<br />
** created a superclass for all displayable managers (vtkMRMLAnnotationDisplayableManager)<br />
** created vtkMRMLAnnotationTextDisplayableManager based on the old qMRMLAnnotationTextManager<br />
** working on the add text node functionality with the new displayable manager<br />
** fixed linking errors appearing on the Slicer Dashboard<br />
* 07/01/10<br />
** re-factored module from miAnnotation to Annotation<br />
** re-integrating functionality without KWWidgets<br />
*** MRMLDisplayableManager was created by Kitware guys and includes base functionality for the re-integration<br />
*** starting with adding text nodes<br />
**** UML diagram for involved classes: [[MiAnnotation_Documentation#Development]] (needs to be checked for logic/manager/mrml pattern consistency) <br />
** added option to set helptext for the module in consistency with qSlicerWidget<br />
* 06/24/10<br />
** Compiling without KWWidgets on Mac OS is now possible.<br />
** Starting to include the functionality of KWWidgets in pure QT code.<br />
** Daniel Haehn took over project from Yong Zhang.<br />
* 06/18/10<br />
** Tutorial is created.<br />
** GetAnnotationMeasurement is modified to return multiple measurements.<br />
** ROI annotation is modified to display extension measurements.<br />
** Bidimensional annotation is modified to display bi-line measurements.<br />
* 06/11/10<br />
** Documentation page is created.<br />
** Bugs for property dialog are fixed.<br />
** Constructions of Bidimensional and Spline annotations are modified using proper control point initialization.<br />
** Bugs for showing values for some annotation types are fixed. <br />
* 06/04/10<br />
** vtkSlicerAnnotationROIManager is implemented.<br />
** vtkSlicerAnnotationTextManager is implemented.<br />
** vtkSlicerAnnotationSplineManager is implemented.<br />
** vtkSlicerAnnotationBidimensionalManager is implemented.<br />
* 05/28/10<br />
** vtkMRMLAnnotationROINode is added;<br />
** vtkMRMLAnnotationBiDimensionalNode is added;<br />
** vtkMRMLAnnotationSplineNode is added.<br />
** Logic and ModuleWidget are modified to include new Nodes<br />
* 05/21/10<br />
** ROI, Text, BiDimensional, and Spline Annotations are initialized.<br />
** fixed BUG: HTML report cannot be saved properly.<br />
* 05/14/10<br />
** fixed BUG: When opening display properties from Sticky note -> reduce frame and enlarge it again by pressing triangle next to title : value and coordinates appear<br />
** fixed BUG: fiducial manager is added.<br />
** fixed BUG: AnnotationMouseModePick/Place are updated.<br />
* 05/07/10<br />
** fixed BUG: Lock does not lock the position of a widget in the 3D Viewer<br />
** fixed BUG: changing coordinates to AngleNode does not have any effects on the Angle Widget.<br />
** fixed BUG: fix coloring for annotation selection<br />
*04/30/10<br />
** fixed BUG: changing control points cannot be done when property dialog is open.<br />
** fixed BUG: annotation is not highlighted when selected.<br />
** fixed BUG: starting from the 2nd annotation, changing the location of the left point for ruler or center point for angle does not update the table properly.<br />
** fixed Bug : changing the center point of angle node does not update table properly<br />
* 04/23/10<br />
** Created a ruler widget manager <br />
* 04/16/10<br />
** Created the new annotation type sticky note, which allows you to enter text independent from the viewer<br />
* 04/09/10<br />
** Modified source code to be compliant with VTK 5.6<br />
** Grid out your buttons (Create Frame)<br />
** Fixed BUG: When changing line color in Display Properties it changes the Text Color<br />
** Added script for testing color setting <br />
** Fixed BUG: Label of line color changes in property window when defining a unselected color<br />
<br />
* 04/02/10<br />
** Fixed BUG: Nothing happens when Property Window is open and you press the edit button for another annotation<br />
** Restructured Annotation MRML<br />
** Fixed Bug: Resetting of Lines and Points does not work correctly GetNumberOfLines > 0 <br />
<br />
* 03/26/10<br />
** The property restoration is now implemented properly.<br />
** Property Modification is re-designed to simplify the operation.<br />
** Removed bug: ruler/angle disappear after adding fiducials <br />
** Removed BUG: in property dialog, when editing the text, the character is entered from right to left.<br />
** include lock annotation into option button (use same logic as for new (De)select All button)<br />
** For each annotation type provide list outlining which display property can be changed, which cannot , and which one you do not know <br />
** Resolved BUG: When saving a report with a file name that already exists then the following message appears in the command shell "Error: cannot make directory" and directory with files is not updated<br />
** Resolved BUG: Annotation Properties: (Un)selected color is initially white even though widget in 3D viewer is different<br />
** Resolved BUG: Select Color window does not show the correct color<br />
** Resolved BUG: Selected and Unselected Color are switched<br />
** Define Tooltips for fiducial, angle, ruler,report, save mrml button<br />
** In table: Add proper tool tip for visualization and edit button<br />
** Resolved BUG: when saving report with out ending html to the file name - icons will not be saved under Linux<br />
** Created Test Module for testing miAnnotation logic<br />
** In collaboration with Nicole Aucoin figured out line display bug in 3D Viewer <br />
** Use the Kitware slider and colorPicker under Display Property<br />
** Fixed BUG: Slicer crashes when creating an annotation while Display properties is open, and when closing the property window and then pressing edit for the new annotation<br />
<br />
* 03/19/10<br />
** In the property window display properties are shown via collapsed frame by default<br />
** List all attributes for text/point/line and implement those that can be modified<br />
** Fixed BUG: When pressing the property button warning messages pop up in my command shell <br />
** Annotation Properties: For Angle and Ruler Widget also shows now values of AnnotationDisplayNode and AnnotationControlPointsNode<br />
** Change design of html report <br />
** Implemented text edition and update for ruler and angle widgets.<br />
** Changed the default mouse mode icon to MousePick.<br />
** Modified Report Dialog to avoid horizontal slider when screen shot is included in the report.<br />
** Removed multiple warning messages.<br />
** Fixed Bug in Report: empty text fields are displayed without boundaries <br />
** Ruler Distance is now displayed just in mm <br />
** After talking to BWH changed name of tool from Reporting to miAnnotation<br />
* 03/12/10<br />
** Created icons for:<br />
*** edit conditioning for all annotation types (done), <br />
*** mouse mode icons, pause, play, cancel, ok/done, (Un)lock (done)<br />
*** new the annotation types poly line, spline with control points, volume information extractor, and sticky note (done)<br />
*** Modify fiducial icon just to show one star and change save annotation icon (done)<br />
*** Modify save annotation and save scene icons (done)<br />
*** Modify move up/down delete icons (done)<br />
** Write 5 page, double column, AMIA paper about Reporting<br />
* 03/05/10<br />
** Removed Warning Messages when compiling<br />
** Fixed Bug: When entering text in property box (under linux) it is entered from right to left instead left to right <br />
** Fixed Bug: Annotation Property: funny behavior with selecting set of digits in a numerical value and typing in a numeric value - only the first digit gets change.<br />
** Fixed Bug: Value of Angle node is not update in table<br />
** Fixed Bug: Updating the value in the table slows down the operations<br />
** Changed the default ruler from 1mm to 500mm.<br />
** Angle Widget is added by manually clicking three points on the viewer. The angle value is now shown in the table. The behavior of the angle button is in the "toggle down" state until all three control points are set<br />
** When selecting annotation in table, color of annotation in 3D Viewer changes to selected color <br />
** Revised "add ruler" button to click-style instead of toggle-style<br />
** When creating a new annotation, set this entry to selected and all other table entries to unselected<br />
** (De) Select All button: change as discussed with Wendy Plesniak, BWH, to option button with proper logic<br />
** Setting color/selected color for individual Ruler and Angle widgets in property dialog<br />
** Fixed Bug: hiding/unhiding ruler and angle annotations<br />
** Change display property for each annotation individually<br />
** Lots of warning messages when compiling code<br />
* 02/26/10<br />
** Created pop up window showing screen shot<br />
** Manual editing of coordinates via "Property Window"<br />
** Resolved column width problem in table ([http://wiki.na-mic.org/Wiki/index.php/File:Screenshot-Form.JPG original problem], [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_TableV2.png second screen shot problem])<br />
** Fixed bug where hide icon changed size in table<br />
** Include icons when saving html report in a directory with the same name as the html file<br />
** [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_GUI.png Reorganized GUI] based on feedback from Wendy Plesniak, BWH <br />
** Include screen shots (if any) in the report (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_ReportV1.png an example])<br />
** Fixed the following bug: After resizing the 3D Window taking a screen shot only displays the window with the original size (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Window.png screen shot]) <br />
** Fixed Bug: Value update of ruler widget is slow <br />
** Text defined in property box now shows up in table<br />
** Integrated vtkMRMLAnnotationAngleNode with AngleWidget<br />
** Added new buttons to create frame based on feedback from BWH <br />
* 02/19/10 <br />
** Implement a general structure for vtkMRMLAnnotation*Node<br />
** Work together with Kitware to resolve QT Table layout problem <br />
** Allow defining long text annotations for each widget<br />
** Improve user interaction through pop up windows when trying to modify an existing annotation <br />
** Creating and removing ruler now works correctly <br />
** Use correct label format to display measurement values in Annotation Property window <br />
** Created a "Save annotation" Window<br />
** Fixed changing icon size in table (see original [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Table-IconProblem.png screen shot] )<br />
** Fixed slicer crashing closing the property window <br />
** Renamed and resized columns in Table<br />
*02/12/10 removed bugs related to table buttons, linked button to angle widget and ruler widget<br />
*02/05/10 implemented "Save Annotation Report" button and "Move up/down" buttons; added extra column in the report table for visibility; modified annotation property dialog; implemented button-click in the table.<br />
*01/29/10 implemented functionality for "Annotation Property Modification" button, "Create Report" button, and integrated new icons for buttons.<br />
*01/22/10 Set up the source control for the reporting module; implemented functionality for "Select All" button, "Visible" button, and "Delete" button in the GUI; created new icons for buttons<br />
*01/15/10 Organized biweekly Tcon <br />
*01/08/10 Participated in all week All Hands Meeting in Utah; Expanded QT interface with functionality to set seeds in images; Defined a final MRML Structure for storing annotation. <br />
*01/01/10 Generated a [[Media:SlicerAM QtAnnotation.png | GUI interface]] via QT for the annotation module. [[Projects:ARRA:SlicerAM#Widget_related_action_items | Reviewed ]] all VTK Widgets related to annotation. <br />
*12/25/09 Created [[ 2010_Winter_Project_Week_mComment | project ]] and organized [[ AHM2010:AnnotationBreakout | break out session ]] at AHM meeting. Coordinated efforts with BWH team in preparation of the meeting. <br />
*12/18/09 Held workshop to integrate AMI into 3D Slicer. Hired new person to implement AMI in Slicer. <br />
*12/11/09 [[ Projects:ARRA:SlicerAM_RSNA09Report | Summary ]] of tools demoed at RSNA <br />
*12/04/09 Visited RSNA to review annotation tools by GE, Siemens & Phillips. Connected to caBIG AIM project to see how we can make use of their data scheme <br />
*11/29/09 Created GUI for MarkUp module <br />
*11/20/09 Design MRML Structure of Annotation and MarkUp Module<br />
*11/13/09 Organize [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]] Session<br />
*11/06/09 Designed User Interface , Meet with Julien Finet and Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Participated in Qt-Tcon, Interviewed candidate at Almaden, coordinated efforts with Nicole Aucoin <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<br />
<br />
= Feature Request =<br />
== VTK Widgets ==<br />
* For further detail go [[ Projects:ARRA:SlicerAM:KWWidgets | here ]]<br />
<br />
== QT Related ==<br />
* Submit bugs and feature request via [http://na-mic.org/Mantis/search.php?project_id=1&category=QtGUI&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 Mantis]<br />
* Feature requests that may open discussions can be added [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/OpenDiscussions here]<br />
<br />
== Daniel ==<br />
All features/issues are listed here: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
=== Known issues ===<br />
* MRML<br />
** <strike>After loading of scene, the annotations are not displayed in the hierarchy tree anymore</strike><br />
** Load scene does not display 3D widgets, Import scene does<br />
** After importing or load, the user has to click on the widget to enable the connection between tree entry and widget<br />
* Annotations<br />
** Property dialog does not work yet and might crash<br />
** Pick mode does not work correctly, if placement was paused and resumed (the first picked coordinate gets lost)<br />
** <strike>Screenshot imagedata does not get saved on Scene save</strike><br />
* GUI<br />
** if moving an annotation up or down inside a hierarchy, the tree gets confused<br />
** Drag and drop does not work<br />
** <strike>after creating hierarchies, the selected item does not reflect the hierarchy which new annotations get added to</strike><br />
** save buttons not implemented<br />
** <strike>widget intersections do not work</strike><br />
** <strike>Slicer4 crashes on exit after annotations were placed and the scene was not closed manually prior exiting Slicer</strike><br />
<br />
==== Feedback by Users ====<br />
* Ron<br />
<pre><br />
1. I sometime like the fiducials to be spheres, not crosses. In Slicer 3 we had a whole list of options. Can I have them for Slicer4? Can I also change their size?<br />
2. The ruler has different colors in the 3D view and in the slice views. That is wrong.<br />
3. The properties popup require a lot of clicking, including double click. Usability will need to be optimized.<br />
4. No drag and drop in the module.<br />
5. text annotation: arrow in the slice view, but not in the 3d view (see attached)<br />
6. text is not in the box in the slice view<br />
7. the font is butt-ugly. In addition, part of the letter n is cut off by the t. The space between the capital V and the e is too big<br />
8. Slicer 3 let you jump to a fiducial location by right clicking in the list in the module.<br />
9. Also, The ruler does have issues with visibility, when the slice is rendered as well. See attached screensnapshot: little dots to the left, no dots to the right.<br />
</pre><br />
* Isaiah<br />
<pre><br />
1) need "selected" parameter for each fiducial, separate from visibility. It's used as boolean inclusion criteria in several modules - in my case DTI FiducialSeeding but also some other ones like segmentation and for CLI modules.<br />
2) need to set properties for groups of fiducials at once. This is tricky because the hierarchy is generic, but ability to set all parameters for a group of fiducials in one place is important.<br />
3) meta visibility control is helpful but maybe not imperative, ie show/hide a whole group but still maintain the individual visibility settings.<br />
4) flicker of fiducials in 2d-view slice whenever other fiducial is moved across that slice. I have two coplanar fiducials in coronal slice, and move a third back/forth across the axial slice. Each time the third crosses the coronal there is a noticeable flicker of the two fiducials in-plane.<br />
5) positioning with decimal precision rather than integer?<br />
6) the persistent-drag mouse interaction in both 2d and 3d is not ideal (at least to me).<br />
7) deleting a hierarchy with ~30 fiducials incurs a noticeable delay around 7s. I compiled with the standard (debug mode?) instructions on x86, ubuntu 10.04.<br />
8) there are some strange mouse interactions when placing in the 3d view after clicking the "cancel" or "accept" buttons. for example, the first time I create a list it works fine: one click to place each. However, if I stop, delete, and start adding again then it doesn't work the same way: the first click makes a fiducial, but subsequent clicks only occasionally place new fidus. I think the problem is that the interactor is selecting the new first fiducial even if the mouse is very far away - can click on the other side of the screen and drag that fiducial, even after pressing "stop" again.<br />
8a) minor style: is it possible to use stop-sign or something else rather than the current x-in-circle for "cancel"?... my brain sees that as the fiducial button 1/2 the time :)<br />
9) I'm confused by the edit properties display (window) for fiducials. What is the purpose for each tab: text, points, lines? points seems to be a place for a list, but x/y/z is empty and position is instead displayed under "Measurement value" on the text tab.<br />
</pre><br />
<br />
==== Meeting with Ron 05/06/11 ====<br />
Nicole and Daniel met with Ron to discuss usability issues and future development.<br />
<br />
<br />
* <strike>Ron would like the 3d sphere to be the default setting for the glyphs.</strike> (H)<br />
* Change the mouse cursor when in place mode, use the images from the mouse modes toolbar icons. (H)<br />
* Text annotations <br />
** line breaks for long text, automatic (H)<br />
** show some of the text (first 20chars?) in the fiducial text box with ... to denote more visible in the Qt interface (M)<br />
** sometimes don't want an arrow head (M)<br />
** consolidate the text and fiducials into one conceptual package allowing turning on/off the text box, detaching it, leader, etc. (L)<br />
** get the text working in 2d slice windows (H)<br />
* Set one time place as the default in the annotation module (add a persistent radio button?) (H)<br />
* Rulers <br />
** expose the tick mark options in the GUI (need to support mice, humans, galaxies) (L)<br />
** use the NeuroDTI example data set from Ron's drop box (H)<br />
** 3d tumor model when measuring it's diameter, the measurement text is hidden inside of it, add an option to position the text at and end or in the middle (H)<br />
** toggle label visibility (M)<br />
* Bidim <br />
** does RECIST need to be orthogonal? Yes<br />
** add the word orthogonal to the tooltip (done)<br />
** make a new icon with a quarter circle between two arms of the axes and use it (L)<br />
* Reformat widget <br />
** estimated time to implementation? (email sent to Will S.) <br />
* Save <br />
** <strike>Ron vetoed the Save panel in the Annotation module, all saving is to be done via the centralised widget (H)</strike><br />
** <strike>take out the save/load buttons, move the report buttons to another part of the GUI (H)</strike><br />
** add the screen snapshot functionality (especially the over sampling) to the scene views pop up window and bring it up from the shortcut box in the lower left of the GUI (this may need some infrastructure changes) (H)<br />
* Workflows <br />
** use the DTI Tumor scene as a sample (M)<br />
** when Ron created the views, each scene view is a workflow end point <br />
** once the annotation functionality is all there, Nicole will meet with Ron and add the annotations to the scene view and save a new scene, and also document the process for usability improvements and testing (M)<br />
* ROIs<br />
** see the Slicer3 crop volume module for a good initialization method: make the ROI node and then update it by clicking in the 2d slice (M)<br />
** 2d annotation ROI -> label map (H)<br />
** match handle colours of the widget to 2d elements in the GUI (H)<br />
** implement the fit ROI to volume functionality (L)<br />
*** once it is included in volume rendering in Slicer 4 please take a look at this functionality - if it is easy to import than it has high priority <br />
* Scene views (M)<br />
** test the Neuro DTI file on Slicer4 <br />
** create a new Slicer4 Annotation Testing mrml file and upload it to the drop box<br />
<br />
= Display Properties of Widgets =<br />
* Unavailable / Unknown:<br />
** Set text colors for Ruler and Angle Widget <br />
** Get/Set glyph scale / point size for point display node<br />
** Get/Set text opacity/ambient/diffuse/specular from text display node <br />
** Color of "angle line" cannot be defined <br />
* Available:<br />
** Get/Set text colors from display node<br />
** Get/Set text scale from display node<br />
** Get/Set point colors from point display node<br />
** Get/Set point opacity/ambient/diffuse/specular from point display node<br />
** Get/Set line colors from line display node<br />
** Get/Set line width/opacity/ambient/diffuse/specular from line display node<br />
** Get text format for angle and ruler</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation&diff=67139Projects:ARRA:miAnnotation2011-05-13T15:41:03Z<p>Pohl: /* Meeting with Ron 05/06/11 */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
<br />
= Aim =<br />
[[Image:SlicerAM_QtAnnotation.png|241px|right|Annotation Module]]<br />
<br />
Medical images often contain a wealth of information, such as anatomy and pathology, not explicitly accessible. One way to address this issue is via image annotation and markup. We propose to create a comprehensive framework for annotation and markup within 3D Slicer, enabling users to capture structured information easily. Furthermore, we will develop schemas for saving and recovering this information into and from XNAT, allowing queries of larger data sets of medical scans. This tool will provide clinicians with a relatively simple way to capture information latent in medical scans, and also to select micro-cohorts of medical scans for studying diseases.<br />
<br />
= Research Plan =<br />
3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include: <br />
* a rich set of geometric objects for improved visual differentiation between annotations<br />
* markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection<br />
* entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologiesand <br />
* a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT.<br />
<br />
We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region.<br />
<br />
The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values. <br />
<br />
Both modules are accompanied by training materials and documentation to ensure usability.<br />
=Design of Module=<br />
* Current [[Media:AMI-GUI-Design.ppt | GUI ]] outline - [[Media:SlicerAM QtAnnotation.png | Screenhot]] in Slicer <br />
* Suggested [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] outline<br />
* Wendy's Mouse Mode sketches http://www.slicer.org/slicerWiki/index.php/Slicer4:UIDesign:MouseModeSketches<br />
<br />
= Documentation=<br />
* [[ miAnnotation_Documentation | Documentation ]] of the module<br />
* Using the [[Media:Slicer4_miAnnotation.ppt | module]] with corresponding data ([[Media:Slicer4_miAnnotation_data.zip | sample data]] )<br />
<br />
=Key Personnel=<br />
10% Kilian Pohl (UPenn) <BR><br />
95% Daniel Haehn (UPenn) <BR><br />
5% Dominique Belhachemi (UPenn) <BR><br />
<br />
=Past Contributors=<br />
Yong Zhang (IBM) <br><br />
<br />
=Events=<br />
* 05/18/10 [[Media:miAnnotation_May2010_Yong.pdf | Presentation]] at the Department of Healthcare Informatics, IBM, Almaden<br />
* 12/16/09 - 12/17/09 [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]]<br />
* 01/06/10 [[AHM2010:AnnotationBreakout | Break out session]] at AHM 2010<br />
* 01/19/10 Biweekly Annotation Tcon from 4:00 - 5:00 pm EST (next meeting 2/9): Tel: (218) 862-1115 Conference ID: 348265#, [https://www.lotuslive.com/join?schedid=4572317 Desktop Sharing ]<br />
* 08/30/10 Budget Year 1 [[ Projects:ARRA:SlicerAM:Meeting20100831 | Review meeting ]]<br />
<br />
=Progress=<br />
* 13/05/11<br />
** MRML: add required modified events for certain display properties<br />
** add opacity slider to text properties in the property dialog<br />
** add a spacer to the property dialog to have a consistent design for text, point and line properties<br />
** add label position to the display node<br />
** add utility methods to get the text, point, line display nodes for a given mrml node id<br />
** handle the main annotation types when setting them active in the selection node<br />
** hook up the text opacity, the point material properties. Grey out the line tab if no line display node. Add the point values to the table in the points tab<br />
** removed the Save panel from the module GUI and moved the buttons for report and screenshot in the edit toolbar (this might change at one point)<br />
** added a storage node for the annotation screen snapshot node to properly save the screenshots<br />
** cleanup of annotation snapshot nodes<br />
** use the text opacity, the point material properties<br />
** add value constraints for several sliders in the property dialog<br />
** MRML: add new method SetControlPoint(id, coords) without the visible and selected flags<br />
** property dialog now complete for text, point, line! (not for hierarchies yet)<br />
* 06/05/11<br />
** fiducials are now shown the same way in 2D and 3D<br />
** the property dialog is connected to configure point colors and glyph types for fiducials<br />
** it is possible to add text to a fiducial in 3D<br />
** meeting with Ron to discuss further development and usability issues<br />
* 04/29/11<br />
** fixed the flickering when placing or interacting with fiducials and rulers<br />
** removed some obsolete render calls to enhance performance<br />
* 04/22/11<br />
** worked together with Nicole<br />
*** finally fixed the crash on Slicer exit<br />
*** investigated why MRMLScene import works fine with the annotations but MRMLScene load does not<br />
**** first success: import and load mrml scenes now both load the annotations in 2D and 3D<br />
* 04/15/11<br />
** Maintenance<br />
* 04/08/11<br />
** Maintenance<br />
* 04/01/11<br />
** Maintenance<br />
* 03/25/11<br />
** Maintenance<br />
* 03/18/11<br />
** Work on MRML Load/Save issues (Nicole)<br />
** Maintenance<br />
* 03/11/11<br />
** Work on hierarchies (Nicole)<br />
** Maintenance<br />
* 03/04/11<br />
** Maintenance<br />
* 02/25/11<br />
** Maintenance<br />
* 02/18/11<br />
** Maintenance<br />
** Communication with Daniel Rubin from Stanford to plan AIM integration<br />
*** provided Annotation MRML examples<br />
* 02/11/11<br />
** Maintenance<br />
* 02/04/11<br />
** Clarified how to add Node Selectors for Annotations to the GUI of 3rd Party 3D Slicer Modules<br />
*** Kitware provided necessary infrastructure<br />
*** Proof of Concept in the new CropVolume module with ROI Annotations (Andriy)<br />
** Clearing up the Annotation Storage Node Tests (Nicole)<br />
* 01/28/11<br />
** Presented Annotation module and SceneView module at NAC EAB Meeting<br />
** Smaller bugs and maintenance<br />
** Meeting with Nicole and Alex concerning the final API of hierarchies in Slicer4<br />
* 01/21/11<br />
** Re-activated ROI annotation with backwards compatibility to the old vtkMRMLROINode<br />
*** Tested successfully with a scene from Slicer3<br />
*** Provided documentation to relevant people<br />
** Rulers now support the measurement tape behavior<br />
** Changed the UPenn logo<br />
** Several smaller fixes<br />
** provided Wendy with Screenshots for NAC Poster<br />
*** [[File:Annotation.png|none|thumb|The current state of the Annotation module.]]<br />
*** [[File:Report.png|none|thumb|The report dialog.]]<br />
** Found displayableManager inconsistency between 2D and 3D and the MRML Node Added Event<br />
** MRML backwards compatibility fix for all Annotations<br />
*** new tag "visible", old tag "visibility"<br />
* 01/14/11<br />
** Attended NA-MIC project week<br />
**Enabled picking when placing annotations in 3D. <br />
**Fixed display of ruler intersections. <br />
**Added new icons. <br />
**Use only three seeds to place bidimensional widgets which results in more stability. <br />
**It is also now possible to add annotations to the toplevel hierarchy after another hierarchy was created by clicking in an empty space of the treeView.<br />
**Re-added the ROI functionality, so now we have 5 widgets<br />
**Ruler: enabled display of ticks (measuring tape mode) in 2D and 3D<br />
* 01/07/11<br />
** re-factored the annotation module in terms of changes in the Slicer4 environment<br />
*** ready for the new developer release<br />
** worked on the outsourced SceneView functionality to make SceneViews survive round-trips (mrml load and save)<br />
* 12/31/10<br />
** Maintenance<br />
** Documentation<br />
* 12/24/10<br />
** Maintenance<br />
** Received the first bug reports of potential users<br />
*** Updated bugtracker<br />
* 12/17/10<br />
** Extended Report functionality<br />
*** now includes screenshots<br />
*** shows the hierarchies<br />
** Sorting of Annotations now possible<br />
** Widgets:<br />
*** added the 3D representation of rulers<br />
*** removed the vtkInteractorRecorder hack by placing the widgets programmatically<br />
** Outsourced the former integrated scene snapshot functionality<br />
*** Wrote a new module called SceneViews<br />
*** vtkMRMLSceneViewNode replaces the old snapshot node and includes thumbnail, description..<br />
**** is not part of the displayable framework anymore<br />
** Added confirmation questions prior to removing annotations<br />
** Worked on MRML save/load<br />
** Updated the priority list: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
** Added a section for known issues: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation#Known_issues<br />
** Annotation module Lines of Code (without .ui files and no blank lines): 24820<br />
* 12/10/10<br />
** Changed some things in the MRML architecture to enhance encapsulation<br />
*** Adding new Annotations should be easier now<br />
** Lock selected, toggle visibility of selected and delete selected implemented<br />
** Report functionality works again<br />
*** Added support to print and export as a HTML report<br />
* 12/03/10<br />
** Added icons to the hierarchy tree<br />
** Configured a proxy model to display only vtkMRMLAnnotationHierarchyNodes and vtkMRMLAnnotationNodes in the hierarchy tree<br />
** Smaller layout fixes<br />
** Added 'full layout' thumbnail functionality to Annotation snapshots<br />
** Removed the old table and replaced fully by the treeView<br />
** Over 1000 of lines of code were removed<br />
*** Hierarchies are now usable<br />
*** [[File:Annotationscreenshot.png|none|thumb|Screenshot of an example Annotation using the new features]]<br />
* 11/26/10<br />
** Added functionality to the module logic to be able to place fiducials programmatically<br />
*** This will be used if one presses the 'p' key on a slice view<br />
** Re-activated the text annotation<br />
*** Used vtkCaptionWidget instead vtkTextWidget to be able to have an anchorpoint in 3D space<br />
** The scene, camera and view nodes are now hidden from the hierarchy tree<br />
*** The toplevel annotation hierarchy is the new root and also hidden<br />
** Added functionality to show Annotation snapshot nodes in the hierarchy tree<br />
*** This required adding the original snapshot node to the displayable framework (as a workaround)<br />
*** Later, we will add thumbnail and description directly to vtkMRMLNode, so that a screenshot can be attached to every MRML node<br />
** Overall code polishing in terms of code conventions<br />
*** including the destruction of the frozen seedWidget on Slicer exit<br />
* 11/19/10<br />
** Small fixes to the Annotation snapshot functionality<br />
** New functionality: reset view to when the annotation was placed<br />
** Derived qMRMLAnnotationTreeWidget and qMRMLSceneAnnotationModel to support hierarchies in the module<br />
*** the widgets let us customize the look and feel of the treeWidget<br />
*** in this context, fixed the creation of hierarchies to a specific order in the scene (which is need for the widget)<br />
*** the Annotation hierarchy nodes and the Annotations get already displayed in the treeWidget<br />
** Fixed stack smashing in connection with a recently introduced compiler flag<br />
* 11/12/10<br />
** All widgets are now restricted to the current renderer which makes the interaction more robust.<br />
** Fixed funky behavior after fiducials were placed.<br />
** New functionality: Annotation snapshots (screenshot + description + scene snapshot) implemented.<br />
*** [[File:snapshot1.png|none|thumb|The new annotation snapshot functionality (part 1)]] [[File:snapshot2.png|none|thumb|The new annotation snapshot functionality (part 2)]]<br />
* 11/05/10<br />
** Widget Design Fiesta http://www.na-mic.org/Wiki/index.php/WidgetDesign2010<br />
** Widget intersections works nearly perfectly<br />
*** Unfortunately, only for centered datasets<br />
** Restrict ruler placement to the current renderer works now. This means, the ruler does not disappear when one point moves outside the sliceview.<br />
* 10/29/10<br />
** Lightbox view works for Fiducials<br />
*** Other widgets have to be refined to be used in a lightbox view due to inconsistent VTK API. The VTK Widget Fiesta should target this.<br />
** Widget intersections in the works, not perfectly working yet.<br />
* 10/22/10<br />
** Priority list for the December release of Slicer4: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
* 10/15/10<br />
** Adopting the old TCL logic to enable 2D widgets on reformats and lightbox views<br />
*** Still working on the lightbox view (very close)<br />
* 10/08/10<br />
** Code-cleanup of the logic class - any old and clumsy code was removed.<br />
** Introducing the StringHolder design pattern [(c) Steve] to always show measurement correctly in the GUI.<br />
** Widget creation now works on Unix aswell.<br />
** Added the RegisterNodes method to register node classes when the scene gets attached to the logic class.<br />
** Hierarchy nodes get added when an annotation is created (code workflow to be optimized).<br />
** Configured a nightly build system to build and test the annotation code every night on a SPL workstation.<br />
* 10/01/10<br />
** The hierarchy changes will replace the table in the GUI with a tree widget<br />
*** Added a tree widget to the GUI additionally to the table to display both during the transition stage<br />
** Fixed the follower bug, which sometimes dragged the second controlpoint of a widget behind when the other controlpoint was moved.<br />
* 9/24/10<br />
** Wrote performance test for vtkWidgets in a standalone VTK mode<br />
*** compared performance in Slicer against standalone VTK<br />
*** rendering of text labels was found to be the performance hog, disabling these labels increases performance inside and outside Slicer dramatically<br />
** Meeting between Wendy, Nicole, Steve and Daniel to review the Annotation module status<br />
*** Notes: [[Projects:ARRA:SlicerAM:Meeting20100921]]<br />
** Annotation hierarchy in the works<br />
* 9/17/10<br />
** 2D placement of Rulers, Bidimensional and Fiducials works now<br />
*** The widgets get synchronized along the slice viewers and the 3D view<br />
** Added extra layer on top of vtkWidgets and vtkWidgetRepresentations to add some extra functionality like calculating distances of measurement correctly in 2D<br />
*** bidimensional measurement and rulers now show the correct distance also in 2D<br />
** Fixed possible null pointer exception in vtkMRMLSliceLogic<br />
** Refactored GetSliceOffSet from vtkMRMLSliceLogic to vtkMRMLSliceNode<br />
* 9/10/10<br />
** 2D placement of Annotations in the works<br />
*** change of the underlying architecture to use one displayableManager for 2D and 3D resulting in less code duplication<br />
*** to perform the changes, all annotations but fiducials were disabled for now<br />
* 9/3/10<br />
** Annotation module status review and planning meeting took place in 1249 Boylston<br />
*** Agenda and Notes: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:Meeting20100831<br />
**** includes new generated class diagram<br />
** Property dialog updated (see screenshot)<br />
*** [[File:Annotationpropertydialog.png|none|thumb|The new annotation property dialog.]]<br />
*** first MRML-Widget synchronization works, the text tab in the property dialog works well with the text widget<br />
** new icons for bidimensional measurement and ROI by Wendy<br />
** updated ctkColorPickerButton to include the ability to disable the setting of the color hexcode as the buttontext to avoid the workaround we had in the annotation module<br />
* 08/27/10<br />
** added a work-around to initialize renderer properly resulting in improved display of annotations in 3D viewer<br />
** cleaned up the code (more then 1000 lines of code where obsolete)<br />
** updating property dialog, which includes revisiting the displayableManagers to support MRML and widget updates<br />
* 08/20/10<br />
** fiducials and sticky node work now<br />
** ruler and spline work now<br />
*** spline widget causes problems b/c after one spline was placed, no interaction with 3D scene possible<br />
** ROI works now<br />
** all annotations now can be placed to examine widget behavior<br />
** started working on a new interface for the property dialog<br />
** consolidated experts for 2D slice displayableManagers<br />
** started working on synchronizing the widgets with MRML display nodes<br />
** fixed GUI problem: the table did not expand even if there was free space in the module frame. now it works.<br />
* 08/13/10<br />
** Wendy, Nicole and Daniel discussed how to integrate mouse modes of Slicer into Annotation module and vice versa. Solution is a widget which appears in the Annotation module panel but can also be shown outside of it as a toplevel window in Slicer (maybe with keybinding), see here: http://wiki.na-mic.org/Wiki/index.php/File:Widget.png<br />
** current status (workflow, user places seeds and widget appears):<br />
*** angle annotations work (note: the widget did not support programmatical placement. a trick is used to place the widget where the user has clicked)<br />
*** text annotations work<br />
** modified vtkMRMLInteractionNode to have a customTag for place modes not only from annotation module but all modules<br />
* 08/06/10<br />
** Enhanced the workflow for creating text annotations. This approach should serve as a general framework for all annotations (sequence diagram available http://wiki.na-mic.org/Wiki/index.php/File:TextAnnotationWorkflow.png)<br />
** modified vtkMRMLInteractionNode to support the place modes for the annotations<br />
*** meet with Wendy next week to discuss integration<br />
** added a click counter class to support the creation of widgets with multiple clicks (very generalized to support all annotations)<br />
*** plan is to place seeds before the actual widget gets created<br />
* 07/29/10<br />
** Created an extra layer called vtkMRMLAnnotationDisplayableManager which serves as a superclass for all specific Annotation displayableManagers. F.e. the vtkMRMLAnnotationTextDisplayableManager is now really lightweight.<br />
** Coordinated with Wendy to add additions interaction modes to vtkMRMLInteractionNode to support different interaction types for different annotations. This will happen under the hood, so the user sees only the "place" mode.<br />
** Got together with members of the 3D & Advanced Imaging Lab at UPENN to investigate how commercial products realize annotations (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:vtkWidgets#How_do_they_do_it.3F).<br />
** Interactive placement of text annotations is now possible. This should be the standard way of placing annotations for all available types.<br />
** Added a test for the creation of a text annotation and its widget without a displayableManager (vtkMRMLAnnotationTextNodeAndWidgetTest1)<br />
** Removed initial values from AnnotationNodes due to different seg-fault errors when properties where not initialized. To cut down confusion, no initializations are now necessary.<br />
* 07/22/10 <br />
** Meeting of Nicole, Steve and Daniel to talk about architecture<br />
*** biggest change is the introduction of a hierarchy for annotation<br />
**** more information and discussion during the tcon:[[Projects:ARRA:miAnnotation_Meeting_07202010|Meeting / Weekly meeting]]<br />
** fixed AnnotationTextDisplayableManager to support multiple text annotations<br />
** added a test for the AnnotationTextDisplayableManager<br />
** property dialog for annotations gets displayed again, nevertheless the connection to the MRML display nodes needs further work<br />
* 07/15/10<br />
** add text nodes using the new displayable manager architecture is now possible<br />
*** nevertheless, full functionality is not restored yet<br />
** added fiducial displayable manager<br />
** new Slicer bug tracker category: Annotations<br />
*** filed open bugs and feature requests - please add all new requests there<br />
* 07/08/10<br />
** moved tests to Testing/Cxx<br />
** created a superclass for all displayable managers (vtkMRMLAnnotationDisplayableManager)<br />
** created vtkMRMLAnnotationTextDisplayableManager based on the old qMRMLAnnotationTextManager<br />
** working on the add text node functionality with the new displayable manager<br />
** fixed linking errors appearing on the Slicer Dashboard<br />
* 07/01/10<br />
** re-factored module from miAnnotation to Annotation<br />
** re-integrating functionality without KWWidgets<br />
*** MRMLDisplayableManager was created by Kitware guys and includes base functionality for the re-integration<br />
*** starting with adding text nodes<br />
**** UML diagram for involved classes: [[MiAnnotation_Documentation#Development]] (needs to be checked for logic/manager/mrml pattern consistency) <br />
** added option to set helptext for the module in consistency with qSlicerWidget<br />
* 06/24/10<br />
** Compiling without KWWidgets on Mac OS is now possible.<br />
** Starting to include the functionality of KWWidgets in pure QT code.<br />
** Daniel Haehn took over project from Yong Zhang.<br />
* 06/18/10<br />
** Tutorial is created.<br />
** GetAnnotationMeasurement is modified to return multiple measurements.<br />
** ROI annotation is modified to display extension measurements.<br />
** Bidimensional annotation is modified to display bi-line measurements.<br />
* 06/11/10<br />
** Documentation page is created.<br />
** Bugs for property dialog are fixed.<br />
** Constructions of Bidimensional and Spline annotations are modified using proper control point initialization.<br />
** Bugs for showing values for some annotation types are fixed. <br />
* 06/04/10<br />
** vtkSlicerAnnotationROIManager is implemented.<br />
** vtkSlicerAnnotationTextManager is implemented.<br />
** vtkSlicerAnnotationSplineManager is implemented.<br />
** vtkSlicerAnnotationBidimensionalManager is implemented.<br />
* 05/28/10<br />
** vtkMRMLAnnotationROINode is added;<br />
** vtkMRMLAnnotationBiDimensionalNode is added;<br />
** vtkMRMLAnnotationSplineNode is added.<br />
** Logic and ModuleWidget are modified to include new Nodes<br />
* 05/21/10<br />
** ROI, Text, BiDimensional, and Spline Annotations are initialized.<br />
** fixed BUG: HTML report cannot be saved properly.<br />
* 05/14/10<br />
** fixed BUG: When opening display properties from Sticky note -> reduce frame and enlarge it again by pressing triangle next to title : value and coordinates appear<br />
** fixed BUG: fiducial manager is added.<br />
** fixed BUG: AnnotationMouseModePick/Place are updated.<br />
* 05/07/10<br />
** fixed BUG: Lock does not lock the position of a widget in the 3D Viewer<br />
** fixed BUG: changing coordinates to AngleNode does not have any effects on the Angle Widget.<br />
** fixed BUG: fix coloring for annotation selection<br />
*04/30/10<br />
** fixed BUG: changing control points cannot be done when property dialog is open.<br />
** fixed BUG: annotation is not highlighted when selected.<br />
** fixed BUG: starting from the 2nd annotation, changing the location of the left point for ruler or center point for angle does not update the table properly.<br />
** fixed Bug : changing the center point of angle node does not update table properly<br />
* 04/23/10<br />
** Created a ruler widget manager <br />
* 04/16/10<br />
** Created the new annotation type sticky note, which allows you to enter text independent from the viewer<br />
* 04/09/10<br />
** Modified source code to be compliant with VTK 5.6<br />
** Grid out your buttons (Create Frame)<br />
** Fixed BUG: When changing line color in Display Properties it changes the Text Color<br />
** Added script for testing color setting <br />
** Fixed BUG: Label of line color changes in property window when defining a unselected color<br />
<br />
* 04/02/10<br />
** Fixed BUG: Nothing happens when Property Window is open and you press the edit button for another annotation<br />
** Restructured Annotation MRML<br />
** Fixed Bug: Resetting of Lines and Points does not work correctly GetNumberOfLines > 0 <br />
<br />
* 03/26/10<br />
** The property restoration is now implemented properly.<br />
** Property Modification is re-designed to simplify the operation.<br />
** Removed bug: ruler/angle disappear after adding fiducials <br />
** Removed BUG: in property dialog, when editing the text, the character is entered from right to left.<br />
** include lock annotation into option button (use same logic as for new (De)select All button)<br />
** For each annotation type provide list outlining which display property can be changed, which cannot , and which one you do not know <br />
** Resolved BUG: When saving a report with a file name that already exists then the following message appears in the command shell "Error: cannot make directory" and directory with files is not updated<br />
** Resolved BUG: Annotation Properties: (Un)selected color is initially white even though widget in 3D viewer is different<br />
** Resolved BUG: Select Color window does not show the correct color<br />
** Resolved BUG: Selected and Unselected Color are switched<br />
** Define Tooltips for fiducial, angle, ruler,report, save mrml button<br />
** In table: Add proper tool tip for visualization and edit button<br />
** Resolved BUG: when saving report with out ending html to the file name - icons will not be saved under Linux<br />
** Created Test Module for testing miAnnotation logic<br />
** In collaboration with Nicole Aucoin figured out line display bug in 3D Viewer <br />
** Use the Kitware slider and colorPicker under Display Property<br />
** Fixed BUG: Slicer crashes when creating an annotation while Display properties is open, and when closing the property window and then pressing edit for the new annotation<br />
<br />
* 03/19/10<br />
** In the property window display properties are shown via collapsed frame by default<br />
** List all attributes for text/point/line and implement those that can be modified<br />
** Fixed BUG: When pressing the property button warning messages pop up in my command shell <br />
** Annotation Properties: For Angle and Ruler Widget also shows now values of AnnotationDisplayNode and AnnotationControlPointsNode<br />
** Change design of html report <br />
** Implemented text edition and update for ruler and angle widgets.<br />
** Changed the default mouse mode icon to MousePick.<br />
** Modified Report Dialog to avoid horizontal slider when screen shot is included in the report.<br />
** Removed multiple warning messages.<br />
** Fixed Bug in Report: empty text fields are displayed without boundaries <br />
** Ruler Distance is now displayed just in mm <br />
** After talking to BWH changed name of tool from Reporting to miAnnotation<br />
* 03/12/10<br />
** Created icons for:<br />
*** edit conditioning for all annotation types (done), <br />
*** mouse mode icons, pause, play, cancel, ok/done, (Un)lock (done)<br />
*** new the annotation types poly line, spline with control points, volume information extractor, and sticky note (done)<br />
*** Modify fiducial icon just to show one star and change save annotation icon (done)<br />
*** Modify save annotation and save scene icons (done)<br />
*** Modify move up/down delete icons (done)<br />
** Write 5 page, double column, AMIA paper about Reporting<br />
* 03/05/10<br />
** Removed Warning Messages when compiling<br />
** Fixed Bug: When entering text in property box (under linux) it is entered from right to left instead left to right <br />
** Fixed Bug: Annotation Property: funny behavior with selecting set of digits in a numerical value and typing in a numeric value - only the first digit gets change.<br />
** Fixed Bug: Value of Angle node is not update in table<br />
** Fixed Bug: Updating the value in the table slows down the operations<br />
** Changed the default ruler from 1mm to 500mm.<br />
** Angle Widget is added by manually clicking three points on the viewer. The angle value is now shown in the table. The behavior of the angle button is in the "toggle down" state until all three control points are set<br />
** When selecting annotation in table, color of annotation in 3D Viewer changes to selected color <br />
** Revised "add ruler" button to click-style instead of toggle-style<br />
** When creating a new annotation, set this entry to selected and all other table entries to unselected<br />
** (De) Select All button: change as discussed with Wendy Plesniak, BWH, to option button with proper logic<br />
** Setting color/selected color for individual Ruler and Angle widgets in property dialog<br />
** Fixed Bug: hiding/unhiding ruler and angle annotations<br />
** Change display property for each annotation individually<br />
** Lots of warning messages when compiling code<br />
* 02/26/10<br />
** Created pop up window showing screen shot<br />
** Manual editing of coordinates via "Property Window"<br />
** Resolved column width problem in table ([http://wiki.na-mic.org/Wiki/index.php/File:Screenshot-Form.JPG original problem], [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_TableV2.png second screen shot problem])<br />
** Fixed bug where hide icon changed size in table<br />
** Include icons when saving html report in a directory with the same name as the html file<br />
** [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_GUI.png Reorganized GUI] based on feedback from Wendy Plesniak, BWH <br />
** Include screen shots (if any) in the report (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_ReportV1.png an example])<br />
** Fixed the following bug: After resizing the 3D Window taking a screen shot only displays the window with the original size (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Window.png screen shot]) <br />
** Fixed Bug: Value update of ruler widget is slow <br />
** Text defined in property box now shows up in table<br />
** Integrated vtkMRMLAnnotationAngleNode with AngleWidget<br />
** Added new buttons to create frame based on feedback from BWH <br />
* 02/19/10 <br />
** Implement a general structure for vtkMRMLAnnotation*Node<br />
** Work together with Kitware to resolve QT Table layout problem <br />
** Allow defining long text annotations for each widget<br />
** Improve user interaction through pop up windows when trying to modify an existing annotation <br />
** Creating and removing ruler now works correctly <br />
** Use correct label format to display measurement values in Annotation Property window <br />
** Created a "Save annotation" Window<br />
** Fixed changing icon size in table (see original [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Table-IconProblem.png screen shot] )<br />
** Fixed slicer crashing closing the property window <br />
** Renamed and resized columns in Table<br />
*02/12/10 removed bugs related to table buttons, linked button to angle widget and ruler widget<br />
*02/05/10 implemented "Save Annotation Report" button and "Move up/down" buttons; added extra column in the report table for visibility; modified annotation property dialog; implemented button-click in the table.<br />
*01/29/10 implemented functionality for "Annotation Property Modification" button, "Create Report" button, and integrated new icons for buttons.<br />
*01/22/10 Set up the source control for the reporting module; implemented functionality for "Select All" button, "Visible" button, and "Delete" button in the GUI; created new icons for buttons<br />
*01/15/10 Organized biweekly Tcon <br />
*01/08/10 Participated in all week All Hands Meeting in Utah; Expanded QT interface with functionality to set seeds in images; Defined a final MRML Structure for storing annotation. <br />
*01/01/10 Generated a [[Media:SlicerAM QtAnnotation.png | GUI interface]] via QT for the annotation module. [[Projects:ARRA:SlicerAM#Widget_related_action_items | Reviewed ]] all VTK Widgets related to annotation. <br />
*12/25/09 Created [[ 2010_Winter_Project_Week_mComment | project ]] and organized [[ AHM2010:AnnotationBreakout | break out session ]] at AHM meeting. Coordinated efforts with BWH team in preparation of the meeting. <br />
*12/18/09 Held workshop to integrate AMI into 3D Slicer. Hired new person to implement AMI in Slicer. <br />
*12/11/09 [[ Projects:ARRA:SlicerAM_RSNA09Report | Summary ]] of tools demoed at RSNA <br />
*12/04/09 Visited RSNA to review annotation tools by GE, Siemens & Phillips. Connected to caBIG AIM project to see how we can make use of their data scheme <br />
*11/29/09 Created GUI for MarkUp module <br />
*11/20/09 Design MRML Structure of Annotation and MarkUp Module<br />
*11/13/09 Organize [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]] Session<br />
*11/06/09 Designed User Interface , Meet with Julien Finet and Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Participated in Qt-Tcon, Interviewed candidate at Almaden, coordinated efforts with Nicole Aucoin <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<br />
<br />
= Feature Request =<br />
== VTK Widgets ==<br />
* For further detail go [[ Projects:ARRA:SlicerAM:KWWidgets | here ]]<br />
<br />
== QT Related ==<br />
* Submit bugs and feature request via [http://na-mic.org/Mantis/search.php?project_id=1&category=QtGUI&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 Mantis]<br />
* Feature requests that may open discussions can be added [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/OpenDiscussions here]<br />
<br />
== Daniel ==<br />
All features/issues are listed here: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
=== Known issues ===<br />
* MRML<br />
** <strike>After loading of scene, the annotations are not displayed in the hierarchy tree anymore</strike><br />
** Load scene does not display 3D widgets, Import scene does<br />
** After importing or load, the user has to click on the widget to enable the connection between tree entry and widget<br />
* Annotations<br />
** Property dialog does not work yet and might crash<br />
** Pick mode does not work correctly, if placement was paused and resumed (the first picked coordinate gets lost)<br />
** <strike>Screenshot imagedata does not get saved on Scene save</strike><br />
* GUI<br />
** if moving an annotation up or down inside a hierarchy, the tree gets confused<br />
** Drag and drop does not work<br />
** <strike>after creating hierarchies, the selected item does not reflect the hierarchy which new annotations get added to</strike><br />
** save buttons not implemented<br />
** <strike>widget intersections do not work</strike><br />
** <strike>Slicer4 crashes on exit after annotations were placed and the scene was not closed manually prior exiting Slicer</strike><br />
<br />
==== Feedback by Users ====<br />
* Ron<br />
<pre><br />
1. I sometime like the fiducials to be spheres, not crosses. In Slicer 3 we had a whole list of options. Can I have them for Slicer4? Can I also change their size?<br />
2. The ruler has different colors in the 3D view and in the slice views. That is wrong.<br />
3. The properties popup require a lot of clicking, including double click. Usability will need to be optimized.<br />
4. No drag and drop in the module.<br />
5. text annotation: arrow in the slice view, but not in the 3d view (see attached)<br />
6. text is not in the box in the slice view<br />
7. the font is butt-ugly. In addition, part of the letter n is cut off by the t. The space between the capital V and the e is too big<br />
8. Slicer 3 let you jump to a fiducial location by right clicking in the list in the module.<br />
9. Also, The ruler does have issues with visibility, when the slice is rendered as well. See attached screensnapshot: little dots to the left, no dots to the right.<br />
</pre><br />
* Isaiah<br />
<pre><br />
1) need "selected" parameter for each fiducial, separate from visibility. It's used as boolean inclusion criteria in several modules - in my case DTI FiducialSeeding but also some other ones like segmentation and for CLI modules.<br />
2) need to set properties for groups of fiducials at once. This is tricky because the hierarchy is generic, but ability to set all parameters for a group of fiducials in one place is important.<br />
3) meta visibility control is helpful but maybe not imperative, ie show/hide a whole group but still maintain the individual visibility settings.<br />
4) flicker of fiducials in 2d-view slice whenever other fiducial is moved across that slice. I have two coplanar fiducials in coronal slice, and move a third back/forth across the axial slice. Each time the third crosses the coronal there is a noticeable flicker of the two fiducials in-plane.<br />
5) positioning with decimal precision rather than integer?<br />
6) the persistent-drag mouse interaction in both 2d and 3d is not ideal (at least to me).<br />
7) deleting a hierarchy with ~30 fiducials incurs a noticeable delay around 7s. I compiled with the standard (debug mode?) instructions on x86, ubuntu 10.04.<br />
8) there are some strange mouse interactions when placing in the 3d view after clicking the "cancel" or "accept" buttons. for example, the first time I create a list it works fine: one click to place each. However, if I stop, delete, and start adding again then it doesn't work the same way: the first click makes a fiducial, but subsequent clicks only occasionally place new fidus. I think the problem is that the interactor is selecting the new first fiducial even if the mouse is very far away - can click on the other side of the screen and drag that fiducial, even after pressing "stop" again.<br />
8a) minor style: is it possible to use stop-sign or something else rather than the current x-in-circle for "cancel"?... my brain sees that as the fiducial button 1/2 the time :)<br />
9) I'm confused by the edit properties display (window) for fiducials. What is the purpose for each tab: text, points, lines? points seems to be a place for a list, but x/y/z is empty and position is instead displayed under "Measurement value" on the text tab.<br />
</pre><br />
<br />
==== Meeting with Ron 05/06/11 ====<br />
Nicole and Daniel met with Ron to discuss usability issues and future development.<br />
<br />
<br />
* <strike>Ron would like the 3d sphere to be the default setting for the glyphs.</strike> (H)<br />
* Change the mouse cursor when in place mode, use the images from the mouse modes toolbar icons. (H)<br />
* Text annotations <br />
** line breaks for long text, automatic (H)<br />
** show some of the text (first 20chars?) in the fiducial text box with ... to denote more visible in the Qt interface (M)<br />
** sometimes don't want an arrow head (M)<br />
** consolidate the text and fiducials into one conceptual package allowing turning on/off the text box, detaching it, leader, etc. (L)<br />
** get the text working in 2d slice windows (H)<br />
* Set one time place as the default in the annotation module (add a persistent radio button?) (H)<br />
* Rulers <br />
** expose the tick mark options in the GUI (need to support mice, humans, galaxies) (L)<br />
** use the NeuroDTI example data set from Ron's drop box (H)<br />
** 3d tumor model when measuring it's diameter, the measurement text is hidden inside of it, add an option to position the text at and end or in the middle (H)<br />
** toggle label visibility (M)<br />
* Bidim <br />
** does RECIST need to be orthogonal? Yes<br />
** add the word orthogonal to the tooltip (done)<br />
** make a new icon with a quarter circle between two arms of the axes and use it (L)<br />
* Reformat widget <br />
** estimated time to implementation? (email sent to Will S.) <br />
* Save <br />
** <strike>Ron vetoed the Save panel in the Annotation module, all saving is to be done via the centralised widget (H)</strike><br />
** <strike>take out the save/load buttons, move the report buttons to another part of the GUI (H)</strike><br />
** add the screen snapshot functionality (especially the over sampling) to the scene views pop up window and bring it up from the shortcut box in the lower left of the GUI (this may need some infrastructure changes) (H)<br />
* Workflows <br />
** use the DTI Tumor scene as a sample (M)<br />
** when Ron created the views, each scene view is a workflow end point <br />
** once the annotation functionality is all there, Nicole will meet with Ron and add the annotations to the scene view and save a new scene, and also document the process for usability improvements and testing (M)<br />
* ROIs<br />
** see the Slicer3 crop volume module for a good initialization method: make the ROI node and then update it by clicking in the 2d slice (M)<br />
** 2d annotation ROI -> label map (H)<br />
** match handle colours of the widget to 2d elements in the GUI (H)<br />
** implement the fit ROI to volume functionality (L)<br />
* Scene views (M)<br />
** test the Neuro DTI file on Slicer4 <br />
** create a new Slicer4 Annotation Testing mrml file and upload it to the drop box<br />
<br />
= Display Properties of Widgets =<br />
* Unavailable / Unknown:<br />
** Set text colors for Ruler and Angle Widget <br />
** Get/Set glyph scale / point size for point display node<br />
** Get/Set text opacity/ambient/diffuse/specular from text display node <br />
** Color of "angle line" cannot be defined <br />
* Available:<br />
** Get/Set text colors from display node<br />
** Get/Set text scale from display node<br />
** Get/Set point colors from point display node<br />
** Get/Set point opacity/ambient/diffuse/specular from point display node<br />
** Get/Set line colors from line display node<br />
** Get/Set line width/opacity/ambient/diffuse/specular from line display node<br />
** Get text format for angle and ruler</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation&diff=67136Projects:ARRA:miAnnotation2011-05-13T15:23:11Z<p>Pohl: /* Meeting with Ron 05/06/11 */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
<br />
= Aim =<br />
[[Image:SlicerAM_QtAnnotation.png|241px|right|Annotation Module]]<br />
<br />
Medical images often contain a wealth of information, such as anatomy and pathology, not explicitly accessible. One way to address this issue is via image annotation and markup. We propose to create a comprehensive framework for annotation and markup within 3D Slicer, enabling users to capture structured information easily. Furthermore, we will develop schemas for saving and recovering this information into and from XNAT, allowing queries of larger data sets of medical scans. This tool will provide clinicians with a relatively simple way to capture information latent in medical scans, and also to select micro-cohorts of medical scans for studying diseases.<br />
<br />
= Research Plan =<br />
3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include: <br />
* a rich set of geometric objects for improved visual differentiation between annotations<br />
* markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection<br />
* entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologiesand <br />
* a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT.<br />
<br />
We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region.<br />
<br />
The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values. <br />
<br />
Both modules are accompanied by training materials and documentation to ensure usability.<br />
=Design of Module=<br />
* Current [[Media:AMI-GUI-Design.ppt | GUI ]] outline - [[Media:SlicerAM QtAnnotation.png | Screenhot]] in Slicer <br />
* Suggested [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] outline<br />
* Wendy's Mouse Mode sketches http://www.slicer.org/slicerWiki/index.php/Slicer4:UIDesign:MouseModeSketches<br />
<br />
= Documentation=<br />
* [[ miAnnotation_Documentation | Documentation ]] of the module<br />
* Using the [[Media:Slicer4_miAnnotation.ppt | module]] with corresponding data ([[Media:Slicer4_miAnnotation_data.zip | sample data]] )<br />
<br />
=Key Personnel=<br />
10% Kilian Pohl (UPenn) <BR><br />
95% Daniel Haehn (UPenn) <BR><br />
5% Dominique Belhachemi (UPenn) <BR><br />
<br />
=Past Contributors=<br />
Yong Zhang (IBM) <br><br />
<br />
=Events=<br />
* 05/18/10 [[Media:miAnnotation_May2010_Yong.pdf | Presentation]] at the Department of Healthcare Informatics, IBM, Almaden<br />
* 12/16/09 - 12/17/09 [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]]<br />
* 01/06/10 [[AHM2010:AnnotationBreakout | Break out session]] at AHM 2010<br />
* 01/19/10 Biweekly Annotation Tcon from 4:00 - 5:00 pm EST (next meeting 2/9): Tel: (218) 862-1115 Conference ID: 348265#, [https://www.lotuslive.com/join?schedid=4572317 Desktop Sharing ]<br />
* 08/30/10 Budget Year 1 [[ Projects:ARRA:SlicerAM:Meeting20100831 | Review meeting ]]<br />
<br />
=Progress=<br />
* 06/05/11<br />
** fiducials are now shows the same way in 2D and 3D<br />
** the property dialog is connected to configure point colors and glyph types for fiducials<br />
** it is possible to add text to a fiducial in 3D<br />
** meeting with Ron to discuss further development and usability issues<br />
* 04/29/11<br />
** fixed the flickering when placing or interacting with fiducials and rulers<br />
** removed some obsolete render calls to enhance performance<br />
* 04/22/11<br />
** worked together with Nicole<br />
*** finally fixed the crash on Slicer exit<br />
*** investigated why MRMLScene import works fine with the annotations but MRMLScene load does not<br />
**** first success: import and load mrml scenes now both load the annotations in 2D and 3D<br />
* 04/15/11<br />
** Maintenance<br />
* 04/08/11<br />
** Maintenance<br />
* 04/01/11<br />
** Maintenance<br />
* 03/25/11<br />
** Maintenance<br />
* 03/18/11<br />
** Work on MRML Load/Save issues (Nicole)<br />
** Maintenance<br />
* 03/11/11<br />
** Work on hierarchies (Nicole)<br />
** Maintenance<br />
* 03/04/11<br />
** Maintenance<br />
* 02/25/11<br />
** Maintenance<br />
* 02/18/11<br />
** Maintenance<br />
** Communication with Daniel Rubin from Stanford to plan AIM integration<br />
*** provided Annotation MRML examples<br />
* 02/11/11<br />
** Maintenance<br />
* 02/04/11<br />
** Clarified how to add Node Selectors for Annotations to the GUI of 3rd Party 3D Slicer Modules<br />
*** Kitware provided necessary infrastructure<br />
*** Proof of Concept in the new CropVolume module with ROI Annotations (Andriy)<br />
** Clearing up the Annotation Storage Node Tests (Nicole)<br />
* 01/28/11<br />
** Presented Annotation module and SceneView module at NAC EAB Meeting<br />
** Smaller bugs and maintenance<br />
** Meeting with Nicole and Alex concerning the final API of hierarchies in Slicer4<br />
* 01/21/11<br />
** Re-activated ROI annotation with backwards compatibility to the old vtkMRMLROINode<br />
*** Tested successfully with a scene from Slicer3<br />
*** Provided documentation to relevant people<br />
** Rulers now support the measurement tape behavior<br />
** Changed the UPenn logo<br />
** Several smaller fixes<br />
** provided Wendy with Screenshots for NAC Poster<br />
*** [[File:Annotation.png|none|thumb|The current state of the Annotation module.]]<br />
*** [[File:Report.png|none|thumb|The report dialog.]]<br />
** Found displayableManager inconsistency between 2D and 3D and the MRML Node Added Event<br />
** MRML backwards compatibility fix for all Annotations<br />
*** new tag "visible", old tag "visibility"<br />
* 01/14/11<br />
** Attended NA-MIC project week<br />
**Enabled picking when placing annotations in 3D. <br />
**Fixed display of ruler intersections. <br />
**Added new icons. <br />
**Use only three seeds to place bidimensional widgets which results in more stability. <br />
**It is also now possible to add annotations to the toplevel hierarchy after another hierarchy was created by clicking in an empty space of the treeView.<br />
**Re-added the ROI functionality, so now we have 5 widgets<br />
**Ruler: enabled display of ticks (measuring tape mode) in 2D and 3D<br />
* 01/07/11<br />
** re-factored the annotation module in terms of changes in the Slicer4 environment<br />
*** ready for the new developer release<br />
** worked on the outsourced SceneView functionality to make SceneViews survive round-trips (mrml load and save)<br />
* 12/31/10<br />
** Maintenance<br />
** Documentation<br />
* 12/24/10<br />
** Maintenance<br />
** Received the first bug reports of potential users<br />
*** Updated bugtracker<br />
* 12/17/10<br />
** Extended Report functionality<br />
*** now includes screenshots<br />
*** shows the hierarchies<br />
** Sorting of Annotations now possible<br />
** Widgets:<br />
*** added the 3D representation of rulers<br />
*** removed the vtkInteractorRecorder hack by placing the widgets programmatically<br />
** Outsourced the former integrated scene snapshot functionality<br />
*** Wrote a new module called SceneViews<br />
*** vtkMRMLSceneViewNode replaces the old snapshot node and includes thumbnail, description..<br />
**** is not part of the displayable framework anymore<br />
** Added confirmation questions prior to removing annotations<br />
** Worked on MRML save/load<br />
** Updated the priority list: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
** Added a section for known issues: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation#Known_issues<br />
** Annotation module Lines of Code (without .ui files and no blank lines): 24820<br />
* 12/10/10<br />
** Changed some things in the MRML architecture to enhance encapsulation<br />
*** Adding new Annotations should be easier now<br />
** Lock selected, toggle visibility of selected and delete selected implemented<br />
** Report functionality works again<br />
*** Added support to print and export as a HTML report<br />
* 12/03/10<br />
** Added icons to the hierarchy tree<br />
** Configured a proxy model to display only vtkMRMLAnnotationHierarchyNodes and vtkMRMLAnnotationNodes in the hierarchy tree<br />
** Smaller layout fixes<br />
** Added 'full layout' thumbnail functionality to Annotation snapshots<br />
** Removed the old table and replaced fully by the treeView<br />
** Over 1000 of lines of code were removed<br />
*** Hierarchies are now usable<br />
*** [[File:Annotationscreenshot.png|none|thumb|Screenshot of an example Annotation using the new features]]<br />
* 11/26/10<br />
** Added functionality to the module logic to be able to place fiducials programmatically<br />
*** This will be used if one presses the 'p' key on a slice view<br />
** Re-activated the text annotation<br />
*** Used vtkCaptionWidget instead vtkTextWidget to be able to have an anchorpoint in 3D space<br />
** The scene, camera and view nodes are now hidden from the hierarchy tree<br />
*** The toplevel annotation hierarchy is the new root and also hidden<br />
** Added functionality to show Annotation snapshot nodes in the hierarchy tree<br />
*** This required adding the original snapshot node to the displayable framework (as a workaround)<br />
*** Later, we will add thumbnail and description directly to vtkMRMLNode, so that a screenshot can be attached to every MRML node<br />
** Overall code polishing in terms of code conventions<br />
*** including the destruction of the frozen seedWidget on Slicer exit<br />
* 11/19/10<br />
** Small fixes to the Annotation snapshot functionality<br />
** New functionality: reset view to when the annotation was placed<br />
** Derived qMRMLAnnotationTreeWidget and qMRMLSceneAnnotationModel to support hierarchies in the module<br />
*** the widgets let us customize the look and feel of the treeWidget<br />
*** in this context, fixed the creation of hierarchies to a specific order in the scene (which is need for the widget)<br />
*** the Annotation hierarchy nodes and the Annotations get already displayed in the treeWidget<br />
** Fixed stack smashing in connection with a recently introduced compiler flag<br />
* 11/12/10<br />
** All widgets are now restricted to the current renderer which makes the interaction more robust.<br />
** Fixed funky behavior after fiducials were placed.<br />
** New functionality: Annotation snapshots (screenshot + description + scene snapshot) implemented.<br />
*** [[File:snapshot1.png|none|thumb|The new annotation snapshot functionality (part 1)]] [[File:snapshot2.png|none|thumb|The new annotation snapshot functionality (part 2)]]<br />
* 11/05/10<br />
** Widget Design Fiesta http://www.na-mic.org/Wiki/index.php/WidgetDesign2010<br />
** Widget intersections works nearly perfectly<br />
*** Unfortunately, only for centered datasets<br />
** Restrict ruler placement to the current renderer works now. This means, the ruler does not disappear when one point moves outside the sliceview.<br />
* 10/29/10<br />
** Lightbox view works for Fiducials<br />
*** Other widgets have to be refined to be used in a lightbox view due to inconsistent VTK API. The VTK Widget Fiesta should target this.<br />
** Widget intersections in the works, not perfectly working yet.<br />
* 10/22/10<br />
** Priority list for the December release of Slicer4: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
* 10/15/10<br />
** Adopting the old TCL logic to enable 2D widgets on reformats and lightbox views<br />
*** Still working on the lightbox view (very close)<br />
* 10/08/10<br />
** Code-cleanup of the logic class - any old and clumsy code was removed.<br />
** Introducing the StringHolder design pattern [(c) Steve] to always show measurement correctly in the GUI.<br />
** Widget creation now works on Unix aswell.<br />
** Added the RegisterNodes method to register node classes when the scene gets attached to the logic class.<br />
** Hierarchy nodes get added when an annotation is created (code workflow to be optimized).<br />
** Configured a nightly build system to build and test the annotation code every night on a SPL workstation.<br />
* 10/01/10<br />
** The hierarchy changes will replace the table in the GUI with a tree widget<br />
*** Added a tree widget to the GUI additionally to the table to display both during the transition stage<br />
** Fixed the follower bug, which sometimes dragged the second controlpoint of a widget behind when the other controlpoint was moved.<br />
* 9/24/10<br />
** Wrote performance test for vtkWidgets in a standalone VTK mode<br />
*** compared performance in Slicer against standalone VTK<br />
*** rendering of text labels was found to be the performance hog, disabling these labels increases performance inside and outside Slicer dramatically<br />
** Meeting between Wendy, Nicole, Steve and Daniel to review the Annotation module status<br />
*** Notes: [[Projects:ARRA:SlicerAM:Meeting20100921]]<br />
** Annotation hierarchy in the works<br />
* 9/17/10<br />
** 2D placement of Rulers, Bidimensional and Fiducials works now<br />
*** The widgets get synchronized along the slice viewers and the 3D view<br />
** Added extra layer on top of vtkWidgets and vtkWidgetRepresentations to add some extra functionality like calculating distances of measurement correctly in 2D<br />
*** bidimensional measurement and rulers now show the correct distance also in 2D<br />
** Fixed possible null pointer exception in vtkMRMLSliceLogic<br />
** Refactored GetSliceOffSet from vtkMRMLSliceLogic to vtkMRMLSliceNode<br />
* 9/10/10<br />
** 2D placement of Annotations in the works<br />
*** change of the underlying architecture to use one displayableManager for 2D and 3D resulting in less code duplication<br />
*** to perform the changes, all annotations but fiducials were disabled for now<br />
* 9/3/10<br />
** Annotation module status review and planning meeting took place in 1249 Boylston<br />
*** Agenda and Notes: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:Meeting20100831<br />
**** includes new generated class diagram<br />
** Property dialog updated (see screenshot)<br />
*** [[File:Annotationpropertydialog.png|none|thumb|The new annotation property dialog.]]<br />
*** first MRML-Widget synchronization works, the text tab in the property dialog works well with the text widget<br />
** new icons for bidimensional measurement and ROI by Wendy<br />
** updated ctkColorPickerButton to include the ability to disable the setting of the color hexcode as the buttontext to avoid the workaround we had in the annotation module<br />
* 08/27/10<br />
** added a work-around to initialize renderer properly resulting in improved display of annotations in 3D viewer<br />
** cleaned up the code (more then 1000 lines of code where obsolete)<br />
** updating property dialog, which includes revisiting the displayableManagers to support MRML and widget updates<br />
* 08/20/10<br />
** fiducials and sticky node work now<br />
** ruler and spline work now<br />
*** spline widget causes problems b/c after one spline was placed, no interaction with 3D scene possible<br />
** ROI works now<br />
** all annotations now can be placed to examine widget behavior<br />
** started working on a new interface for the property dialog<br />
** consolidated experts for 2D slice displayableManagers<br />
** started working on synchronizing the widgets with MRML display nodes<br />
** fixed GUI problem: the table did not expand even if there was free space in the module frame. now it works.<br />
* 08/13/10<br />
** Wendy, Nicole and Daniel discussed how to integrate mouse modes of Slicer into Annotation module and vice versa. Solution is a widget which appears in the Annotation module panel but can also be shown outside of it as a toplevel window in Slicer (maybe with keybinding), see here: http://wiki.na-mic.org/Wiki/index.php/File:Widget.png<br />
** current status (workflow, user places seeds and widget appears):<br />
*** angle annotations work (note: the widget did not support programmatical placement. a trick is used to place the widget where the user has clicked)<br />
*** text annotations work<br />
** modified vtkMRMLInteractionNode to have a customTag for place modes not only from annotation module but all modules<br />
* 08/06/10<br />
** Enhanced the workflow for creating text annotations. This approach should serve as a general framework for all annotations (sequence diagram available http://wiki.na-mic.org/Wiki/index.php/File:TextAnnotationWorkflow.png)<br />
** modified vtkMRMLInteractionNode to support the place modes for the annotations<br />
*** meet with Wendy next week to discuss integration<br />
** added a click counter class to support the creation of widgets with multiple clicks (very generalized to support all annotations)<br />
*** plan is to place seeds before the actual widget gets created<br />
* 07/29/10<br />
** Created an extra layer called vtkMRMLAnnotationDisplayableManager which serves as a superclass for all specific Annotation displayableManagers. F.e. the vtkMRMLAnnotationTextDisplayableManager is now really lightweight.<br />
** Coordinated with Wendy to add additions interaction modes to vtkMRMLInteractionNode to support different interaction types for different annotations. This will happen under the hood, so the user sees only the "place" mode.<br />
** Got together with members of the 3D & Advanced Imaging Lab at UPENN to investigate how commercial products realize annotations (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:vtkWidgets#How_do_they_do_it.3F).<br />
** Interactive placement of text annotations is now possible. This should be the standard way of placing annotations for all available types.<br />
** Added a test for the creation of a text annotation and its widget without a displayableManager (vtkMRMLAnnotationTextNodeAndWidgetTest1)<br />
** Removed initial values from AnnotationNodes due to different seg-fault errors when properties where not initialized. To cut down confusion, no initializations are now necessary.<br />
* 07/22/10 <br />
** Meeting of Nicole, Steve and Daniel to talk about architecture<br />
*** biggest change is the introduction of a hierarchy for annotation<br />
**** more information and discussion during the tcon:[[Projects:ARRA:miAnnotation_Meeting_07202010|Meeting / Weekly meeting]]<br />
** fixed AnnotationTextDisplayableManager to support multiple text annotations<br />
** added a test for the AnnotationTextDisplayableManager<br />
** property dialog for annotations gets displayed again, nevertheless the connection to the MRML display nodes needs further work<br />
* 07/15/10<br />
** add text nodes using the new displayable manager architecture is now possible<br />
*** nevertheless, full functionality is not restored yet<br />
** added fiducial displayable manager<br />
** new Slicer bug tracker category: Annotations<br />
*** filed open bugs and feature requests - please add all new requests there<br />
* 07/08/10<br />
** moved tests to Testing/Cxx<br />
** created a superclass for all displayable managers (vtkMRMLAnnotationDisplayableManager)<br />
** created vtkMRMLAnnotationTextDisplayableManager based on the old qMRMLAnnotationTextManager<br />
** working on the add text node functionality with the new displayable manager<br />
** fixed linking errors appearing on the Slicer Dashboard<br />
* 07/01/10<br />
** re-factored module from miAnnotation to Annotation<br />
** re-integrating functionality without KWWidgets<br />
*** MRMLDisplayableManager was created by Kitware guys and includes base functionality for the re-integration<br />
*** starting with adding text nodes<br />
**** UML diagram for involved classes: [[MiAnnotation_Documentation#Development]] (needs to be checked for logic/manager/mrml pattern consistency) <br />
** added option to set helptext for the module in consistency with qSlicerWidget<br />
* 06/24/10<br />
** Compiling without KWWidgets on Mac OS is now possible.<br />
** Starting to include the functionality of KWWidgets in pure QT code.<br />
** Daniel Haehn took over project from Yong Zhang.<br />
* 06/18/10<br />
** Tutorial is created.<br />
** GetAnnotationMeasurement is modified to return multiple measurements.<br />
** ROI annotation is modified to display extension measurements.<br />
** Bidimensional annotation is modified to display bi-line measurements.<br />
* 06/11/10<br />
** Documentation page is created.<br />
** Bugs for property dialog are fixed.<br />
** Constructions of Bidimensional and Spline annotations are modified using proper control point initialization.<br />
** Bugs for showing values for some annotation types are fixed. <br />
* 06/04/10<br />
** vtkSlicerAnnotationROIManager is implemented.<br />
** vtkSlicerAnnotationTextManager is implemented.<br />
** vtkSlicerAnnotationSplineManager is implemented.<br />
** vtkSlicerAnnotationBidimensionalManager is implemented.<br />
* 05/28/10<br />
** vtkMRMLAnnotationROINode is added;<br />
** vtkMRMLAnnotationBiDimensionalNode is added;<br />
** vtkMRMLAnnotationSplineNode is added.<br />
** Logic and ModuleWidget are modified to include new Nodes<br />
* 05/21/10<br />
** ROI, Text, BiDimensional, and Spline Annotations are initialized.<br />
** fixed BUG: HTML report cannot be saved properly.<br />
* 05/14/10<br />
** fixed BUG: When opening display properties from Sticky note -> reduce frame and enlarge it again by pressing triangle next to title : value and coordinates appear<br />
** fixed BUG: fiducial manager is added.<br />
** fixed BUG: AnnotationMouseModePick/Place are updated.<br />
* 05/07/10<br />
** fixed BUG: Lock does not lock the position of a widget in the 3D Viewer<br />
** fixed BUG: changing coordinates to AngleNode does not have any effects on the Angle Widget.<br />
** fixed BUG: fix coloring for annotation selection<br />
*04/30/10<br />
** fixed BUG: changing control points cannot be done when property dialog is open.<br />
** fixed BUG: annotation is not highlighted when selected.<br />
** fixed BUG: starting from the 2nd annotation, changing the location of the left point for ruler or center point for angle does not update the table properly.<br />
** fixed Bug : changing the center point of angle node does not update table properly<br />
* 04/23/10<br />
** Created a ruler widget manager <br />
* 04/16/10<br />
** Created the new annotation type sticky note, which allows you to enter text independent from the viewer<br />
* 04/09/10<br />
** Modified source code to be compliant with VTK 5.6<br />
** Grid out your buttons (Create Frame)<br />
** Fixed BUG: When changing line color in Display Properties it changes the Text Color<br />
** Added script for testing color setting <br />
** Fixed BUG: Label of line color changes in property window when defining a unselected color<br />
<br />
* 04/02/10<br />
** Fixed BUG: Nothing happens when Property Window is open and you press the edit button for another annotation<br />
** Restructured Annotation MRML<br />
** Fixed Bug: Resetting of Lines and Points does not work correctly GetNumberOfLines > 0 <br />
<br />
* 03/26/10<br />
** The property restoration is now implemented properly.<br />
** Property Modification is re-designed to simplify the operation.<br />
** Removed bug: ruler/angle disappear after adding fiducials <br />
** Removed BUG: in property dialog, when editing the text, the character is entered from right to left.<br />
** include lock annotation into option button (use same logic as for new (De)select All button)<br />
** For each annotation type provide list outlining which display property can be changed, which cannot , and which one you do not know <br />
** Resolved BUG: When saving a report with a file name that already exists then the following message appears in the command shell "Error: cannot make directory" and directory with files is not updated<br />
** Resolved BUG: Annotation Properties: (Un)selected color is initially white even though widget in 3D viewer is different<br />
** Resolved BUG: Select Color window does not show the correct color<br />
** Resolved BUG: Selected and Unselected Color are switched<br />
** Define Tooltips for fiducial, angle, ruler,report, save mrml button<br />
** In table: Add proper tool tip for visualization and edit button<br />
** Resolved BUG: when saving report with out ending html to the file name - icons will not be saved under Linux<br />
** Created Test Module for testing miAnnotation logic<br />
** In collaboration with Nicole Aucoin figured out line display bug in 3D Viewer <br />
** Use the Kitware slider and colorPicker under Display Property<br />
** Fixed BUG: Slicer crashes when creating an annotation while Display properties is open, and when closing the property window and then pressing edit for the new annotation<br />
<br />
* 03/19/10<br />
** In the property window display properties are shown via collapsed frame by default<br />
** List all attributes for text/point/line and implement those that can be modified<br />
** Fixed BUG: When pressing the property button warning messages pop up in my command shell <br />
** Annotation Properties: For Angle and Ruler Widget also shows now values of AnnotationDisplayNode and AnnotationControlPointsNode<br />
** Change design of html report <br />
** Implemented text edition and update for ruler and angle widgets.<br />
** Changed the default mouse mode icon to MousePick.<br />
** Modified Report Dialog to avoid horizontal slider when screen shot is included in the report.<br />
** Removed multiple warning messages.<br />
** Fixed Bug in Report: empty text fields are displayed without boundaries <br />
** Ruler Distance is now displayed just in mm <br />
** After talking to BWH changed name of tool from Reporting to miAnnotation<br />
* 03/12/10<br />
** Created icons for:<br />
*** edit conditioning for all annotation types (done), <br />
*** mouse mode icons, pause, play, cancel, ok/done, (Un)lock (done)<br />
*** new the annotation types poly line, spline with control points, volume information extractor, and sticky note (done)<br />
*** Modify fiducial icon just to show one star and change save annotation icon (done)<br />
*** Modify save annotation and save scene icons (done)<br />
*** Modify move up/down delete icons (done)<br />
** Write 5 page, double column, AMIA paper about Reporting<br />
* 03/05/10<br />
** Removed Warning Messages when compiling<br />
** Fixed Bug: When entering text in property box (under linux) it is entered from right to left instead left to right <br />
** Fixed Bug: Annotation Property: funny behavior with selecting set of digits in a numerical value and typing in a numeric value - only the first digit gets change.<br />
** Fixed Bug: Value of Angle node is not update in table<br />
** Fixed Bug: Updating the value in the table slows down the operations<br />
** Changed the default ruler from 1mm to 500mm.<br />
** Angle Widget is added by manually clicking three points on the viewer. The angle value is now shown in the table. The behavior of the angle button is in the "toggle down" state until all three control points are set<br />
** When selecting annotation in table, color of annotation in 3D Viewer changes to selected color <br />
** Revised "add ruler" button to click-style instead of toggle-style<br />
** When creating a new annotation, set this entry to selected and all other table entries to unselected<br />
** (De) Select All button: change as discussed with Wendy Plesniak, BWH, to option button with proper logic<br />
** Setting color/selected color for individual Ruler and Angle widgets in property dialog<br />
** Fixed Bug: hiding/unhiding ruler and angle annotations<br />
** Change display property for each annotation individually<br />
** Lots of warning messages when compiling code<br />
* 02/26/10<br />
** Created pop up window showing screen shot<br />
** Manual editing of coordinates via "Property Window"<br />
** Resolved column width problem in table ([http://wiki.na-mic.org/Wiki/index.php/File:Screenshot-Form.JPG original problem], [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_TableV2.png second screen shot problem])<br />
** Fixed bug where hide icon changed size in table<br />
** Include icons when saving html report in a directory with the same name as the html file<br />
** [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_GUI.png Reorganized GUI] based on feedback from Wendy Plesniak, BWH <br />
** Include screen shots (if any) in the report (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_ReportV1.png an example])<br />
** Fixed the following bug: After resizing the 3D Window taking a screen shot only displays the window with the original size (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Window.png screen shot]) <br />
** Fixed Bug: Value update of ruler widget is slow <br />
** Text defined in property box now shows up in table<br />
** Integrated vtkMRMLAnnotationAngleNode with AngleWidget<br />
** Added new buttons to create frame based on feedback from BWH <br />
* 02/19/10 <br />
** Implement a general structure for vtkMRMLAnnotation*Node<br />
** Work together with Kitware to resolve QT Table layout problem <br />
** Allow defining long text annotations for each widget<br />
** Improve user interaction through pop up windows when trying to modify an existing annotation <br />
** Creating and removing ruler now works correctly <br />
** Use correct label format to display measurement values in Annotation Property window <br />
** Created a "Save annotation" Window<br />
** Fixed changing icon size in table (see original [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Table-IconProblem.png screen shot] )<br />
** Fixed slicer crashing closing the property window <br />
** Renamed and resized columns in Table<br />
*02/12/10 removed bugs related to table buttons, linked button to angle widget and ruler widget<br />
*02/05/10 implemented "Save Annotation Report" button and "Move up/down" buttons; added extra column in the report table for visibility; modified annotation property dialog; implemented button-click in the table.<br />
*01/29/10 implemented functionality for "Annotation Property Modification" button, "Create Report" button, and integrated new icons for buttons.<br />
*01/22/10 Set up the source control for the reporting module; implemented functionality for "Select All" button, "Visible" button, and "Delete" button in the GUI; created new icons for buttons<br />
*01/15/10 Organized biweekly Tcon <br />
*01/08/10 Participated in all week All Hands Meeting in Utah; Expanded QT interface with functionality to set seeds in images; Defined a final MRML Structure for storing annotation. <br />
*01/01/10 Generated a [[Media:SlicerAM QtAnnotation.png | GUI interface]] via QT for the annotation module. [[Projects:ARRA:SlicerAM#Widget_related_action_items | Reviewed ]] all VTK Widgets related to annotation. <br />
*12/25/09 Created [[ 2010_Winter_Project_Week_mComment | project ]] and organized [[ AHM2010:AnnotationBreakout | break out session ]] at AHM meeting. Coordinated efforts with BWH team in preparation of the meeting. <br />
*12/18/09 Held workshop to integrate AMI into 3D Slicer. Hired new person to implement AMI in Slicer. <br />
*12/11/09 [[ Projects:ARRA:SlicerAM_RSNA09Report | Summary ]] of tools demoed at RSNA <br />
*12/04/09 Visited RSNA to review annotation tools by GE, Siemens & Phillips. Connected to caBIG AIM project to see how we can make use of their data scheme <br />
*11/29/09 Created GUI for MarkUp module <br />
*11/20/09 Design MRML Structure of Annotation and MarkUp Module<br />
*11/13/09 Organize [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]] Session<br />
*11/06/09 Designed User Interface , Meet with Julien Finet and Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Participated in Qt-Tcon, Interviewed candidate at Almaden, coordinated efforts with Nicole Aucoin <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<br />
<br />
= Feature Request =<br />
== VTK Widgets ==<br />
* For further detail go [[ Projects:ARRA:SlicerAM:KWWidgets | here ]]<br />
<br />
== QT Related ==<br />
* Submit bugs and feature request via [http://na-mic.org/Mantis/search.php?project_id=1&category=QtGUI&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 Mantis]<br />
* Feature requests that may open discussions can be added [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/OpenDiscussions here]<br />
<br />
== Daniel ==<br />
All features/issues are listed here: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
=== Known issues ===<br />
* MRML<br />
** <strike>After loading of scene, the annotations are not displayed in the hierarchy tree anymore</strike><br />
** Load scene does not display 3D widgets, Import scene does<br />
** After importing or load, the user has to click on the widget to enable the connection between tree entry and widget<br />
* Annotations<br />
** Property dialog does not work yet and might crash<br />
** Pick mode does not work correctly, if placement was paused and resumed (the first picked coordinate gets lost)<br />
** <strike>Screenshot imagedata does not get saved on Scene save</strike><br />
* GUI<br />
** if moving an annotation up or down inside a hierarchy, the tree gets confused<br />
** Drag and drop does not work<br />
** <strike>after creating hierarchies, the selected item does not reflect the hierarchy which new annotations get added to</strike><br />
** save buttons not implemented<br />
** <strike>widget intersections do not work</strike><br />
** <strike>Slicer4 crashes on exit after annotations were placed and the scene was not closed manually prior exiting Slicer</strike><br />
<br />
==== Feedback by Users ====<br />
* Ron<br />
<pre><br />
1. I sometime like the fiducials to be spheres, not crosses. In Slicer 3 we had a whole list of options. Can I have them for Slicer4? Can I also change their size?<br />
2. The ruler has different colors in the 3D view and in the slice views. That is wrong.<br />
3. The properties popup require a lot of clicking, including double click. Usability will need to be optimized.<br />
4. No drag and drop in the module.<br />
5. text annotation: arrow in the slice view, but not in the 3d view (see attached)<br />
6. text is not in the box in the slice view<br />
7. the font is butt-ugly. In addition, part of the letter n is cut off by the t. The space between the capital V and the e is too big<br />
8. Slicer 3 let you jump to a fiducial location by right clicking in the list in the module.<br />
9. Also, The ruler does have issues with visibility, when the slice is rendered as well. See attached screensnapshot: little dots to the left, no dots to the right.<br />
</pre><br />
* Isaiah<br />
<pre><br />
1) need "selected" parameter for each fiducial, separate from visibility. It's used as boolean inclusion criteria in several modules - in my case DTI FiducialSeeding but also some other ones like segmentation and for CLI modules.<br />
2) need to set properties for groups of fiducials at once. This is tricky because the hierarchy is generic, but ability to set all parameters for a group of fiducials in one place is important.<br />
3) meta visibility control is helpful but maybe not imperative, ie show/hide a whole group but still maintain the individual visibility settings.<br />
4) flicker of fiducials in 2d-view slice whenever other fiducial is moved across that slice. I have two coplanar fiducials in coronal slice, and move a third back/forth across the axial slice. Each time the third crosses the coronal there is a noticeable flicker of the two fiducials in-plane.<br />
5) positioning with decimal precision rather than integer?<br />
6) the persistent-drag mouse interaction in both 2d and 3d is not ideal (at least to me).<br />
7) deleting a hierarchy with ~30 fiducials incurs a noticeable delay around 7s. I compiled with the standard (debug mode?) instructions on x86, ubuntu 10.04.<br />
8) there are some strange mouse interactions when placing in the 3d view after clicking the "cancel" or "accept" buttons. for example, the first time I create a list it works fine: one click to place each. However, if I stop, delete, and start adding again then it doesn't work the same way: the first click makes a fiducial, but subsequent clicks only occasionally place new fidus. I think the problem is that the interactor is selecting the new first fiducial even if the mouse is very far away - can click on the other side of the screen and drag that fiducial, even after pressing "stop" again.<br />
8a) minor style: is it possible to use stop-sign or something else rather than the current x-in-circle for "cancel"?... my brain sees that as the fiducial button 1/2 the time :)<br />
9) I'm confused by the edit properties display (window) for fiducials. What is the purpose for each tab: text, points, lines? points seems to be a place for a list, but x/y/z is empty and position is instead displayed under "Measurement value" on the text tab.<br />
</pre><br />
<br />
==== Meeting with Ron 05/06/11 ====<br />
Nicole and Daniel met with Ron to discuss usability issues and future development.<br />
<br />
<br />
* <strike>Ron would like the 3d sphere to be the default setting for the glyphs.</strike> (H)<br />
* Change the mouse cursor when in place mode, use the images from the mouse modes toolbar icons. (H)<br />
* Text annotations <br />
** line breaks for long text, automatic (L)<br />
** show some of the text (first 20chars?) in the fiducial text box with ... to denote more visible in the Qt interface (M)<br />
** sometimes don't want an arrow head (L)<br />
** consolidate the text and fiducials into one conceptual package allowing turning on/off the text box, detaching it, leader, etc. (L)<br />
** get the text working in 2d slice windows (H)<br />
* Set one time place as the default in the annotation module (add a persistent radio button?) (H)<br />
* Rulers <br />
** expose the tick mark options in the GUI (need to support mice, humans, galaxies) (L)<br />
** use the NeuroDTI example data set from Ron's drop box (H)<br />
** 3d tumor model when measuring it's diameter, the measurement text is hidden inside of it, add an option to position the text at and end or in the middle (L)<br />
** toggle label visibility (M)<br />
* Bidim <br />
** does RECIST need to be orthogonal? Yes<br />
** add the word orthogonal to the tooltip (done)<br />
** make a new icon with a quarter circle between two arms of the axes and use it (L)<br />
* Reformat widget <br />
** estimated time to implementation? (email sent to Will S.) <br />
* Save <br />
** <strike>Ron vetoed the Save panel in the Annotation module, all saving is to be done via the centralised widget (???)</strike><br />
** <strike>take out the save/load buttons, move the report buttons to another part of the GUI (??)</strike><br />
** add the screen snapshot functionality (especially the over sampling) to the scene views pop up window and bring it up from the shortcut box in the lower left of the GUI (this may need some infrastructure changes) (M)<br />
* Workflows <br />
** use the DTI Tumor scene as a sample (M)<br />
** when Ron created the views, each scene view is a workflow end point <br />
** once the annotation functionality is all there, Nicole will meet with Ron and add the annotations to the scene view and save a new scene, and also document the process for usability improvements and testing (M)<br />
* ROIs<br />
** see the Slicer3 crop volume module for a good initialization method: make the ROI node and then update it by clicking in the 2d slice (M)<br />
** 2d annotation ROI -> label map (H)<br />
** match handle colours of the widget to 2d elements in the GUI (H)<br />
** implement the fit ROI to volume functionality (L)<br />
* Scene views (M)<br />
** test the Neuro DTI file on Slicer4 <br />
** create a new Slicer4 Annotation Testing mrml file and upload it to the drop box<br />
<br />
= Display Properties of Widgets =<br />
* Unavailable / Unknown:<br />
** Set text colors for Ruler and Angle Widget <br />
** Get/Set glyph scale / point size for point display node<br />
** Get/Set text opacity/ambient/diffuse/specular from text display node <br />
** Color of "angle line" cannot be defined <br />
* Available:<br />
** Get/Set text colors from display node<br />
** Get/Set text scale from display node<br />
** Get/Set point colors from point display node<br />
** Get/Set point opacity/ambient/diffuse/specular from point display node<br />
** Get/Set line colors from line display node<br />
** Get/Set line width/opacity/ambient/diffuse/specular from line display node<br />
** Get text format for angle and ruler</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation&diff=67134Projects:ARRA:miAnnotation2011-05-13T15:16:44Z<p>Pohl: /* Meeting with Ron 05/06/11 */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
<br />
= Aim =<br />
[[Image:SlicerAM_QtAnnotation.png|241px|right|Annotation Module]]<br />
<br />
Medical images often contain a wealth of information, such as anatomy and pathology, not explicitly accessible. One way to address this issue is via image annotation and markup. We propose to create a comprehensive framework for annotation and markup within 3D Slicer, enabling users to capture structured information easily. Furthermore, we will develop schemas for saving and recovering this information into and from XNAT, allowing queries of larger data sets of medical scans. This tool will provide clinicians with a relatively simple way to capture information latent in medical scans, and also to select micro-cohorts of medical scans for studying diseases.<br />
<br />
= Research Plan =<br />
3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include: <br />
* a rich set of geometric objects for improved visual differentiation between annotations<br />
* markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection<br />
* entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologiesand <br />
* a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT.<br />
<br />
We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region.<br />
<br />
The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values. <br />
<br />
Both modules are accompanied by training materials and documentation to ensure usability.<br />
=Design of Module=<br />
* Current [[Media:AMI-GUI-Design.ppt | GUI ]] outline - [[Media:SlicerAM QtAnnotation.png | Screenhot]] in Slicer <br />
* Suggested [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] outline<br />
* Wendy's Mouse Mode sketches http://www.slicer.org/slicerWiki/index.php/Slicer4:UIDesign:MouseModeSketches<br />
<br />
= Documentation=<br />
* [[ miAnnotation_Documentation | Documentation ]] of the module<br />
* Using the [[Media:Slicer4_miAnnotation.ppt | module]] with corresponding data ([[Media:Slicer4_miAnnotation_data.zip | sample data]] )<br />
<br />
=Key Personnel=<br />
10% Kilian Pohl (UPenn) <BR><br />
95% Daniel Haehn (UPenn) <BR><br />
5% Dominique Belhachemi (UPenn) <BR><br />
<br />
=Past Contributors=<br />
Yong Zhang (IBM) <br><br />
<br />
=Events=<br />
* 05/18/10 [[Media:miAnnotation_May2010_Yong.pdf | Presentation]] at the Department of Healthcare Informatics, IBM, Almaden<br />
* 12/16/09 - 12/17/09 [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]]<br />
* 01/06/10 [[AHM2010:AnnotationBreakout | Break out session]] at AHM 2010<br />
* 01/19/10 Biweekly Annotation Tcon from 4:00 - 5:00 pm EST (next meeting 2/9): Tel: (218) 862-1115 Conference ID: 348265#, [https://www.lotuslive.com/join?schedid=4572317 Desktop Sharing ]<br />
* 08/30/10 Budget Year 1 [[ Projects:ARRA:SlicerAM:Meeting20100831 | Review meeting ]]<br />
<br />
=Progress=<br />
* 06/05/11<br />
** fiducials are now shows the same way in 2D and 3D<br />
** the property dialog is connected to configure point colors and glyph types for fiducials<br />
** it is possible to add text to a fiducial in 3D<br />
** meeting with Ron to discuss further development and usability issues<br />
* 04/29/11<br />
** fixed the flickering when placing or interacting with fiducials and rulers<br />
** removed some obsolete render calls to enhance performance<br />
* 04/22/11<br />
** worked together with Nicole<br />
*** finally fixed the crash on Slicer exit<br />
*** investigated why MRMLScene import works fine with the annotations but MRMLScene load does not<br />
**** first success: import and load mrml scenes now both load the annotations in 2D and 3D<br />
* 04/15/11<br />
** Maintenance<br />
* 04/08/11<br />
** Maintenance<br />
* 04/01/11<br />
** Maintenance<br />
* 03/25/11<br />
** Maintenance<br />
* 03/18/11<br />
** Work on MRML Load/Save issues (Nicole)<br />
** Maintenance<br />
* 03/11/11<br />
** Work on hierarchies (Nicole)<br />
** Maintenance<br />
* 03/04/11<br />
** Maintenance<br />
* 02/25/11<br />
** Maintenance<br />
* 02/18/11<br />
** Maintenance<br />
** Communication with Daniel Rubin from Stanford to plan AIM integration<br />
*** provided Annotation MRML examples<br />
* 02/11/11<br />
** Maintenance<br />
* 02/04/11<br />
** Clarified how to add Node Selectors for Annotations to the GUI of 3rd Party 3D Slicer Modules<br />
*** Kitware provided necessary infrastructure<br />
*** Proof of Concept in the new CropVolume module with ROI Annotations (Andriy)<br />
** Clearing up the Annotation Storage Node Tests (Nicole)<br />
* 01/28/11<br />
** Presented Annotation module and SceneView module at NAC EAB Meeting<br />
** Smaller bugs and maintenance<br />
** Meeting with Nicole and Alex concerning the final API of hierarchies in Slicer4<br />
* 01/21/11<br />
** Re-activated ROI annotation with backwards compatibility to the old vtkMRMLROINode<br />
*** Tested successfully with a scene from Slicer3<br />
*** Provided documentation to relevant people<br />
** Rulers now support the measurement tape behavior<br />
** Changed the UPenn logo<br />
** Several smaller fixes<br />
** provided Wendy with Screenshots for NAC Poster<br />
*** [[File:Annotation.png|none|thumb|The current state of the Annotation module.]]<br />
*** [[File:Report.png|none|thumb|The report dialog.]]<br />
** Found displayableManager inconsistency between 2D and 3D and the MRML Node Added Event<br />
** MRML backwards compatibility fix for all Annotations<br />
*** new tag "visible", old tag "visibility"<br />
* 01/14/11<br />
** Attended NA-MIC project week<br />
**Enabled picking when placing annotations in 3D. <br />
**Fixed display of ruler intersections. <br />
**Added new icons. <br />
**Use only three seeds to place bidimensional widgets which results in more stability. <br />
**It is also now possible to add annotations to the toplevel hierarchy after another hierarchy was created by clicking in an empty space of the treeView.<br />
**Re-added the ROI functionality, so now we have 5 widgets<br />
**Ruler: enabled display of ticks (measuring tape mode) in 2D and 3D<br />
* 01/07/11<br />
** re-factored the annotation module in terms of changes in the Slicer4 environment<br />
*** ready for the new developer release<br />
** worked on the outsourced SceneView functionality to make SceneViews survive round-trips (mrml load and save)<br />
* 12/31/10<br />
** Maintenance<br />
** Documentation<br />
* 12/24/10<br />
** Maintenance<br />
** Received the first bug reports of potential users<br />
*** Updated bugtracker<br />
* 12/17/10<br />
** Extended Report functionality<br />
*** now includes screenshots<br />
*** shows the hierarchies<br />
** Sorting of Annotations now possible<br />
** Widgets:<br />
*** added the 3D representation of rulers<br />
*** removed the vtkInteractorRecorder hack by placing the widgets programmatically<br />
** Outsourced the former integrated scene snapshot functionality<br />
*** Wrote a new module called SceneViews<br />
*** vtkMRMLSceneViewNode replaces the old snapshot node and includes thumbnail, description..<br />
**** is not part of the displayable framework anymore<br />
** Added confirmation questions prior to removing annotations<br />
** Worked on MRML save/load<br />
** Updated the priority list: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
** Added a section for known issues: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation#Known_issues<br />
** Annotation module Lines of Code (without .ui files and no blank lines): 24820<br />
* 12/10/10<br />
** Changed some things in the MRML architecture to enhance encapsulation<br />
*** Adding new Annotations should be easier now<br />
** Lock selected, toggle visibility of selected and delete selected implemented<br />
** Report functionality works again<br />
*** Added support to print and export as a HTML report<br />
* 12/03/10<br />
** Added icons to the hierarchy tree<br />
** Configured a proxy model to display only vtkMRMLAnnotationHierarchyNodes and vtkMRMLAnnotationNodes in the hierarchy tree<br />
** Smaller layout fixes<br />
** Added 'full layout' thumbnail functionality to Annotation snapshots<br />
** Removed the old table and replaced fully by the treeView<br />
** Over 1000 of lines of code were removed<br />
*** Hierarchies are now usable<br />
*** [[File:Annotationscreenshot.png|none|thumb|Screenshot of an example Annotation using the new features]]<br />
* 11/26/10<br />
** Added functionality to the module logic to be able to place fiducials programmatically<br />
*** This will be used if one presses the 'p' key on a slice view<br />
** Re-activated the text annotation<br />
*** Used vtkCaptionWidget instead vtkTextWidget to be able to have an anchorpoint in 3D space<br />
** The scene, camera and view nodes are now hidden from the hierarchy tree<br />
*** The toplevel annotation hierarchy is the new root and also hidden<br />
** Added functionality to show Annotation snapshot nodes in the hierarchy tree<br />
*** This required adding the original snapshot node to the displayable framework (as a workaround)<br />
*** Later, we will add thumbnail and description directly to vtkMRMLNode, so that a screenshot can be attached to every MRML node<br />
** Overall code polishing in terms of code conventions<br />
*** including the destruction of the frozen seedWidget on Slicer exit<br />
* 11/19/10<br />
** Small fixes to the Annotation snapshot functionality<br />
** New functionality: reset view to when the annotation was placed<br />
** Derived qMRMLAnnotationTreeWidget and qMRMLSceneAnnotationModel to support hierarchies in the module<br />
*** the widgets let us customize the look and feel of the treeWidget<br />
*** in this context, fixed the creation of hierarchies to a specific order in the scene (which is need for the widget)<br />
*** the Annotation hierarchy nodes and the Annotations get already displayed in the treeWidget<br />
** Fixed stack smashing in connection with a recently introduced compiler flag<br />
* 11/12/10<br />
** All widgets are now restricted to the current renderer which makes the interaction more robust.<br />
** Fixed funky behavior after fiducials were placed.<br />
** New functionality: Annotation snapshots (screenshot + description + scene snapshot) implemented.<br />
*** [[File:snapshot1.png|none|thumb|The new annotation snapshot functionality (part 1)]] [[File:snapshot2.png|none|thumb|The new annotation snapshot functionality (part 2)]]<br />
* 11/05/10<br />
** Widget Design Fiesta http://www.na-mic.org/Wiki/index.php/WidgetDesign2010<br />
** Widget intersections works nearly perfectly<br />
*** Unfortunately, only for centered datasets<br />
** Restrict ruler placement to the current renderer works now. This means, the ruler does not disappear when one point moves outside the sliceview.<br />
* 10/29/10<br />
** Lightbox view works for Fiducials<br />
*** Other widgets have to be refined to be used in a lightbox view due to inconsistent VTK API. The VTK Widget Fiesta should target this.<br />
** Widget intersections in the works, not perfectly working yet.<br />
* 10/22/10<br />
** Priority list for the December release of Slicer4: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
* 10/15/10<br />
** Adopting the old TCL logic to enable 2D widgets on reformats and lightbox views<br />
*** Still working on the lightbox view (very close)<br />
* 10/08/10<br />
** Code-cleanup of the logic class - any old and clumsy code was removed.<br />
** Introducing the StringHolder design pattern [(c) Steve] to always show measurement correctly in the GUI.<br />
** Widget creation now works on Unix aswell.<br />
** Added the RegisterNodes method to register node classes when the scene gets attached to the logic class.<br />
** Hierarchy nodes get added when an annotation is created (code workflow to be optimized).<br />
** Configured a nightly build system to build and test the annotation code every night on a SPL workstation.<br />
* 10/01/10<br />
** The hierarchy changes will replace the table in the GUI with a tree widget<br />
*** Added a tree widget to the GUI additionally to the table to display both during the transition stage<br />
** Fixed the follower bug, which sometimes dragged the second controlpoint of a widget behind when the other controlpoint was moved.<br />
* 9/24/10<br />
** Wrote performance test for vtkWidgets in a standalone VTK mode<br />
*** compared performance in Slicer against standalone VTK<br />
*** rendering of text labels was found to be the performance hog, disabling these labels increases performance inside and outside Slicer dramatically<br />
** Meeting between Wendy, Nicole, Steve and Daniel to review the Annotation module status<br />
*** Notes: [[Projects:ARRA:SlicerAM:Meeting20100921]]<br />
** Annotation hierarchy in the works<br />
* 9/17/10<br />
** 2D placement of Rulers, Bidimensional and Fiducials works now<br />
*** The widgets get synchronized along the slice viewers and the 3D view<br />
** Added extra layer on top of vtkWidgets and vtkWidgetRepresentations to add some extra functionality like calculating distances of measurement correctly in 2D<br />
*** bidimensional measurement and rulers now show the correct distance also in 2D<br />
** Fixed possible null pointer exception in vtkMRMLSliceLogic<br />
** Refactored GetSliceOffSet from vtkMRMLSliceLogic to vtkMRMLSliceNode<br />
* 9/10/10<br />
** 2D placement of Annotations in the works<br />
*** change of the underlying architecture to use one displayableManager for 2D and 3D resulting in less code duplication<br />
*** to perform the changes, all annotations but fiducials were disabled for now<br />
* 9/3/10<br />
** Annotation module status review and planning meeting took place in 1249 Boylston<br />
*** Agenda and Notes: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:Meeting20100831<br />
**** includes new generated class diagram<br />
** Property dialog updated (see screenshot)<br />
*** [[File:Annotationpropertydialog.png|none|thumb|The new annotation property dialog.]]<br />
*** first MRML-Widget synchronization works, the text tab in the property dialog works well with the text widget<br />
** new icons for bidimensional measurement and ROI by Wendy<br />
** updated ctkColorPickerButton to include the ability to disable the setting of the color hexcode as the buttontext to avoid the workaround we had in the annotation module<br />
* 08/27/10<br />
** added a work-around to initialize renderer properly resulting in improved display of annotations in 3D viewer<br />
** cleaned up the code (more then 1000 lines of code where obsolete)<br />
** updating property dialog, which includes revisiting the displayableManagers to support MRML and widget updates<br />
* 08/20/10<br />
** fiducials and sticky node work now<br />
** ruler and spline work now<br />
*** spline widget causes problems b/c after one spline was placed, no interaction with 3D scene possible<br />
** ROI works now<br />
** all annotations now can be placed to examine widget behavior<br />
** started working on a new interface for the property dialog<br />
** consolidated experts for 2D slice displayableManagers<br />
** started working on synchronizing the widgets with MRML display nodes<br />
** fixed GUI problem: the table did not expand even if there was free space in the module frame. now it works.<br />
* 08/13/10<br />
** Wendy, Nicole and Daniel discussed how to integrate mouse modes of Slicer into Annotation module and vice versa. Solution is a widget which appears in the Annotation module panel but can also be shown outside of it as a toplevel window in Slicer (maybe with keybinding), see here: http://wiki.na-mic.org/Wiki/index.php/File:Widget.png<br />
** current status (workflow, user places seeds and widget appears):<br />
*** angle annotations work (note: the widget did not support programmatical placement. a trick is used to place the widget where the user has clicked)<br />
*** text annotations work<br />
** modified vtkMRMLInteractionNode to have a customTag for place modes not only from annotation module but all modules<br />
* 08/06/10<br />
** Enhanced the workflow for creating text annotations. This approach should serve as a general framework for all annotations (sequence diagram available http://wiki.na-mic.org/Wiki/index.php/File:TextAnnotationWorkflow.png)<br />
** modified vtkMRMLInteractionNode to support the place modes for the annotations<br />
*** meet with Wendy next week to discuss integration<br />
** added a click counter class to support the creation of widgets with multiple clicks (very generalized to support all annotations)<br />
*** plan is to place seeds before the actual widget gets created<br />
* 07/29/10<br />
** Created an extra layer called vtkMRMLAnnotationDisplayableManager which serves as a superclass for all specific Annotation displayableManagers. F.e. the vtkMRMLAnnotationTextDisplayableManager is now really lightweight.<br />
** Coordinated with Wendy to add additions interaction modes to vtkMRMLInteractionNode to support different interaction types for different annotations. This will happen under the hood, so the user sees only the "place" mode.<br />
** Got together with members of the 3D & Advanced Imaging Lab at UPENN to investigate how commercial products realize annotations (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:vtkWidgets#How_do_they_do_it.3F).<br />
** Interactive placement of text annotations is now possible. This should be the standard way of placing annotations for all available types.<br />
** Added a test for the creation of a text annotation and its widget without a displayableManager (vtkMRMLAnnotationTextNodeAndWidgetTest1)<br />
** Removed initial values from AnnotationNodes due to different seg-fault errors when properties where not initialized. To cut down confusion, no initializations are now necessary.<br />
* 07/22/10 <br />
** Meeting of Nicole, Steve and Daniel to talk about architecture<br />
*** biggest change is the introduction of a hierarchy for annotation<br />
**** more information and discussion during the tcon:[[Projects:ARRA:miAnnotation_Meeting_07202010|Meeting / Weekly meeting]]<br />
** fixed AnnotationTextDisplayableManager to support multiple text annotations<br />
** added a test for the AnnotationTextDisplayableManager<br />
** property dialog for annotations gets displayed again, nevertheless the connection to the MRML display nodes needs further work<br />
* 07/15/10<br />
** add text nodes using the new displayable manager architecture is now possible<br />
*** nevertheless, full functionality is not restored yet<br />
** added fiducial displayable manager<br />
** new Slicer bug tracker category: Annotations<br />
*** filed open bugs and feature requests - please add all new requests there<br />
* 07/08/10<br />
** moved tests to Testing/Cxx<br />
** created a superclass for all displayable managers (vtkMRMLAnnotationDisplayableManager)<br />
** created vtkMRMLAnnotationTextDisplayableManager based on the old qMRMLAnnotationTextManager<br />
** working on the add text node functionality with the new displayable manager<br />
** fixed linking errors appearing on the Slicer Dashboard<br />
* 07/01/10<br />
** re-factored module from miAnnotation to Annotation<br />
** re-integrating functionality without KWWidgets<br />
*** MRMLDisplayableManager was created by Kitware guys and includes base functionality for the re-integration<br />
*** starting with adding text nodes<br />
**** UML diagram for involved classes: [[MiAnnotation_Documentation#Development]] (needs to be checked for logic/manager/mrml pattern consistency) <br />
** added option to set helptext for the module in consistency with qSlicerWidget<br />
* 06/24/10<br />
** Compiling without KWWidgets on Mac OS is now possible.<br />
** Starting to include the functionality of KWWidgets in pure QT code.<br />
** Daniel Haehn took over project from Yong Zhang.<br />
* 06/18/10<br />
** Tutorial is created.<br />
** GetAnnotationMeasurement is modified to return multiple measurements.<br />
** ROI annotation is modified to display extension measurements.<br />
** Bidimensional annotation is modified to display bi-line measurements.<br />
* 06/11/10<br />
** Documentation page is created.<br />
** Bugs for property dialog are fixed.<br />
** Constructions of Bidimensional and Spline annotations are modified using proper control point initialization.<br />
** Bugs for showing values for some annotation types are fixed. <br />
* 06/04/10<br />
** vtkSlicerAnnotationROIManager is implemented.<br />
** vtkSlicerAnnotationTextManager is implemented.<br />
** vtkSlicerAnnotationSplineManager is implemented.<br />
** vtkSlicerAnnotationBidimensionalManager is implemented.<br />
* 05/28/10<br />
** vtkMRMLAnnotationROINode is added;<br />
** vtkMRMLAnnotationBiDimensionalNode is added;<br />
** vtkMRMLAnnotationSplineNode is added.<br />
** Logic and ModuleWidget are modified to include new Nodes<br />
* 05/21/10<br />
** ROI, Text, BiDimensional, and Spline Annotations are initialized.<br />
** fixed BUG: HTML report cannot be saved properly.<br />
* 05/14/10<br />
** fixed BUG: When opening display properties from Sticky note -> reduce frame and enlarge it again by pressing triangle next to title : value and coordinates appear<br />
** fixed BUG: fiducial manager is added.<br />
** fixed BUG: AnnotationMouseModePick/Place are updated.<br />
* 05/07/10<br />
** fixed BUG: Lock does not lock the position of a widget in the 3D Viewer<br />
** fixed BUG: changing coordinates to AngleNode does not have any effects on the Angle Widget.<br />
** fixed BUG: fix coloring for annotation selection<br />
*04/30/10<br />
** fixed BUG: changing control points cannot be done when property dialog is open.<br />
** fixed BUG: annotation is not highlighted when selected.<br />
** fixed BUG: starting from the 2nd annotation, changing the location of the left point for ruler or center point for angle does not update the table properly.<br />
** fixed Bug : changing the center point of angle node does not update table properly<br />
* 04/23/10<br />
** Created a ruler widget manager <br />
* 04/16/10<br />
** Created the new annotation type sticky note, which allows you to enter text independent from the viewer<br />
* 04/09/10<br />
** Modified source code to be compliant with VTK 5.6<br />
** Grid out your buttons (Create Frame)<br />
** Fixed BUG: When changing line color in Display Properties it changes the Text Color<br />
** Added script for testing color setting <br />
** Fixed BUG: Label of line color changes in property window when defining a unselected color<br />
<br />
* 04/02/10<br />
** Fixed BUG: Nothing happens when Property Window is open and you press the edit button for another annotation<br />
** Restructured Annotation MRML<br />
** Fixed Bug: Resetting of Lines and Points does not work correctly GetNumberOfLines > 0 <br />
<br />
* 03/26/10<br />
** The property restoration is now implemented properly.<br />
** Property Modification is re-designed to simplify the operation.<br />
** Removed bug: ruler/angle disappear after adding fiducials <br />
** Removed BUG: in property dialog, when editing the text, the character is entered from right to left.<br />
** include lock annotation into option button (use same logic as for new (De)select All button)<br />
** For each annotation type provide list outlining which display property can be changed, which cannot , and which one you do not know <br />
** Resolved BUG: When saving a report with a file name that already exists then the following message appears in the command shell "Error: cannot make directory" and directory with files is not updated<br />
** Resolved BUG: Annotation Properties: (Un)selected color is initially white even though widget in 3D viewer is different<br />
** Resolved BUG: Select Color window does not show the correct color<br />
** Resolved BUG: Selected and Unselected Color are switched<br />
** Define Tooltips for fiducial, angle, ruler,report, save mrml button<br />
** In table: Add proper tool tip for visualization and edit button<br />
** Resolved BUG: when saving report with out ending html to the file name - icons will not be saved under Linux<br />
** Created Test Module for testing miAnnotation logic<br />
** In collaboration with Nicole Aucoin figured out line display bug in 3D Viewer <br />
** Use the Kitware slider and colorPicker under Display Property<br />
** Fixed BUG: Slicer crashes when creating an annotation while Display properties is open, and when closing the property window and then pressing edit for the new annotation<br />
<br />
* 03/19/10<br />
** In the property window display properties are shown via collapsed frame by default<br />
** List all attributes for text/point/line and implement those that can be modified<br />
** Fixed BUG: When pressing the property button warning messages pop up in my command shell <br />
** Annotation Properties: For Angle and Ruler Widget also shows now values of AnnotationDisplayNode and AnnotationControlPointsNode<br />
** Change design of html report <br />
** Implemented text edition and update for ruler and angle widgets.<br />
** Changed the default mouse mode icon to MousePick.<br />
** Modified Report Dialog to avoid horizontal slider when screen shot is included in the report.<br />
** Removed multiple warning messages.<br />
** Fixed Bug in Report: empty text fields are displayed without boundaries <br />
** Ruler Distance is now displayed just in mm <br />
** After talking to BWH changed name of tool from Reporting to miAnnotation<br />
* 03/12/10<br />
** Created icons for:<br />
*** edit conditioning for all annotation types (done), <br />
*** mouse mode icons, pause, play, cancel, ok/done, (Un)lock (done)<br />
*** new the annotation types poly line, spline with control points, volume information extractor, and sticky note (done)<br />
*** Modify fiducial icon just to show one star and change save annotation icon (done)<br />
*** Modify save annotation and save scene icons (done)<br />
*** Modify move up/down delete icons (done)<br />
** Write 5 page, double column, AMIA paper about Reporting<br />
* 03/05/10<br />
** Removed Warning Messages when compiling<br />
** Fixed Bug: When entering text in property box (under linux) it is entered from right to left instead left to right <br />
** Fixed Bug: Annotation Property: funny behavior with selecting set of digits in a numerical value and typing in a numeric value - only the first digit gets change.<br />
** Fixed Bug: Value of Angle node is not update in table<br />
** Fixed Bug: Updating the value in the table slows down the operations<br />
** Changed the default ruler from 1mm to 500mm.<br />
** Angle Widget is added by manually clicking three points on the viewer. The angle value is now shown in the table. The behavior of the angle button is in the "toggle down" state until all three control points are set<br />
** When selecting annotation in table, color of annotation in 3D Viewer changes to selected color <br />
** Revised "add ruler" button to click-style instead of toggle-style<br />
** When creating a new annotation, set this entry to selected and all other table entries to unselected<br />
** (De) Select All button: change as discussed with Wendy Plesniak, BWH, to option button with proper logic<br />
** Setting color/selected color for individual Ruler and Angle widgets in property dialog<br />
** Fixed Bug: hiding/unhiding ruler and angle annotations<br />
** Change display property for each annotation individually<br />
** Lots of warning messages when compiling code<br />
* 02/26/10<br />
** Created pop up window showing screen shot<br />
** Manual editing of coordinates via "Property Window"<br />
** Resolved column width problem in table ([http://wiki.na-mic.org/Wiki/index.php/File:Screenshot-Form.JPG original problem], [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_TableV2.png second screen shot problem])<br />
** Fixed bug where hide icon changed size in table<br />
** Include icons when saving html report in a directory with the same name as the html file<br />
** [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_GUI.png Reorganized GUI] based on feedback from Wendy Plesniak, BWH <br />
** Include screen shots (if any) in the report (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_ReportV1.png an example])<br />
** Fixed the following bug: After resizing the 3D Window taking a screen shot only displays the window with the original size (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Window.png screen shot]) <br />
** Fixed Bug: Value update of ruler widget is slow <br />
** Text defined in property box now shows up in table<br />
** Integrated vtkMRMLAnnotationAngleNode with AngleWidget<br />
** Added new buttons to create frame based on feedback from BWH <br />
* 02/19/10 <br />
** Implement a general structure for vtkMRMLAnnotation*Node<br />
** Work together with Kitware to resolve QT Table layout problem <br />
** Allow defining long text annotations for each widget<br />
** Improve user interaction through pop up windows when trying to modify an existing annotation <br />
** Creating and removing ruler now works correctly <br />
** Use correct label format to display measurement values in Annotation Property window <br />
** Created a "Save annotation" Window<br />
** Fixed changing icon size in table (see original [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Table-IconProblem.png screen shot] )<br />
** Fixed slicer crashing closing the property window <br />
** Renamed and resized columns in Table<br />
*02/12/10 removed bugs related to table buttons, linked button to angle widget and ruler widget<br />
*02/05/10 implemented "Save Annotation Report" button and "Move up/down" buttons; added extra column in the report table for visibility; modified annotation property dialog; implemented button-click in the table.<br />
*01/29/10 implemented functionality for "Annotation Property Modification" button, "Create Report" button, and integrated new icons for buttons.<br />
*01/22/10 Set up the source control for the reporting module; implemented functionality for "Select All" button, "Visible" button, and "Delete" button in the GUI; created new icons for buttons<br />
*01/15/10 Organized biweekly Tcon <br />
*01/08/10 Participated in all week All Hands Meeting in Utah; Expanded QT interface with functionality to set seeds in images; Defined a final MRML Structure for storing annotation. <br />
*01/01/10 Generated a [[Media:SlicerAM QtAnnotation.png | GUI interface]] via QT for the annotation module. [[Projects:ARRA:SlicerAM#Widget_related_action_items | Reviewed ]] all VTK Widgets related to annotation. <br />
*12/25/09 Created [[ 2010_Winter_Project_Week_mComment | project ]] and organized [[ AHM2010:AnnotationBreakout | break out session ]] at AHM meeting. Coordinated efforts with BWH team in preparation of the meeting. <br />
*12/18/09 Held workshop to integrate AMI into 3D Slicer. Hired new person to implement AMI in Slicer. <br />
*12/11/09 [[ Projects:ARRA:SlicerAM_RSNA09Report | Summary ]] of tools demoed at RSNA <br />
*12/04/09 Visited RSNA to review annotation tools by GE, Siemens & Phillips. Connected to caBIG AIM project to see how we can make use of their data scheme <br />
*11/29/09 Created GUI for MarkUp module <br />
*11/20/09 Design MRML Structure of Annotation and MarkUp Module<br />
*11/13/09 Organize [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]] Session<br />
*11/06/09 Designed User Interface , Meet with Julien Finet and Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Participated in Qt-Tcon, Interviewed candidate at Almaden, coordinated efforts with Nicole Aucoin <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<br />
<br />
= Feature Request =<br />
== VTK Widgets ==<br />
* For further detail go [[ Projects:ARRA:SlicerAM:KWWidgets | here ]]<br />
<br />
== QT Related ==<br />
* Submit bugs and feature request via [http://na-mic.org/Mantis/search.php?project_id=1&category=QtGUI&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 Mantis]<br />
* Feature requests that may open discussions can be added [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/OpenDiscussions here]<br />
<br />
== Daniel ==<br />
All features/issues are listed here: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
=== Known issues ===<br />
* MRML<br />
** <strike>After loading of scene, the annotations are not displayed in the hierarchy tree anymore</strike><br />
** Load scene does not display 3D widgets, Import scene does<br />
** After importing or load, the user has to click on the widget to enable the connection between tree entry and widget<br />
* Annotations<br />
** Property dialog does not work yet and might crash<br />
** Pick mode does not work correctly, if placement was paused and resumed (the first picked coordinate gets lost)<br />
** <strike>Screenshot imagedata does not get saved on Scene save</strike><br />
* GUI<br />
** if moving an annotation up or down inside a hierarchy, the tree gets confused<br />
** Drag and drop does not work<br />
** <strike>after creating hierarchies, the selected item does not reflect the hierarchy which new annotations get added to</strike><br />
** save buttons not implemented<br />
** <strike>widget intersections do not work</strike><br />
** <strike>Slicer4 crashes on exit after annotations were placed and the scene was not closed manually prior exiting Slicer</strike><br />
<br />
==== Feedback by Users ====<br />
* Ron<br />
<pre><br />
1. I sometime like the fiducials to be spheres, not crosses. In Slicer 3 we had a whole list of options. Can I have them for Slicer4? Can I also change their size?<br />
2. The ruler has different colors in the 3D view and in the slice views. That is wrong.<br />
3. The properties popup require a lot of clicking, including double click. Usability will need to be optimized.<br />
4. No drag and drop in the module.<br />
5. text annotation: arrow in the slice view, but not in the 3d view (see attached)<br />
6. text is not in the box in the slice view<br />
7. the font is butt-ugly. In addition, part of the letter n is cut off by the t. The space between the capital V and the e is too big<br />
8. Slicer 3 let you jump to a fiducial location by right clicking in the list in the module.<br />
9. Also, The ruler does have issues with visibility, when the slice is rendered as well. See attached screensnapshot: little dots to the left, no dots to the right.<br />
</pre><br />
* Isaiah<br />
<pre><br />
1) need "selected" parameter for each fiducial, separate from visibility. It's used as boolean inclusion criteria in several modules - in my case DTI FiducialSeeding but also some other ones like segmentation and for CLI modules.<br />
2) need to set properties for groups of fiducials at once. This is tricky because the hierarchy is generic, but ability to set all parameters for a group of fiducials in one place is important.<br />
3) meta visibility control is helpful but maybe not imperative, ie show/hide a whole group but still maintain the individual visibility settings.<br />
4) flicker of fiducials in 2d-view slice whenever other fiducial is moved across that slice. I have two coplanar fiducials in coronal slice, and move a third back/forth across the axial slice. Each time the third crosses the coronal there is a noticeable flicker of the two fiducials in-plane.<br />
5) positioning with decimal precision rather than integer?<br />
6) the persistent-drag mouse interaction in both 2d and 3d is not ideal (at least to me).<br />
7) deleting a hierarchy with ~30 fiducials incurs a noticeable delay around 7s. I compiled with the standard (debug mode?) instructions on x86, ubuntu 10.04.<br />
8) there are some strange mouse interactions when placing in the 3d view after clicking the "cancel" or "accept" buttons. for example, the first time I create a list it works fine: one click to place each. However, if I stop, delete, and start adding again then it doesn't work the same way: the first click makes a fiducial, but subsequent clicks only occasionally place new fidus. I think the problem is that the interactor is selecting the new first fiducial even if the mouse is very far away - can click on the other side of the screen and drag that fiducial, even after pressing "stop" again.<br />
8a) minor style: is it possible to use stop-sign or something else rather than the current x-in-circle for "cancel"?... my brain sees that as the fiducial button 1/2 the time :)<br />
9) I'm confused by the edit properties display (window) for fiducials. What is the purpose for each tab: text, points, lines? points seems to be a place for a list, but x/y/z is empty and position is instead displayed under "Measurement value" on the text tab.<br />
</pre><br />
<br />
==== Meeting with Ron 05/06/11 ====<br />
Nicole and Daniel met with Ron to discuss usability issues and future development.<br />
<br />
<br />
* Ron would like the 3d sphere to be the default setting for the glyphs. (H)<br />
* Change the mouse cursor when in place mode, use the images from the mouse modes toolbar icons. (H)<br />
* Text annotations <br />
** line breaks for long text, automatic (L)<br />
** show some of the text (first 20chars?) in the fiducial text box with ... to denote more visible in the Qt interface (M)<br />
** sometimes don't want an arrow head (L)<br />
** consolidate the text and fiducials into one conceptual package allowing turning on/off the text box, detaching it, leader, etc. (L)<br />
** get the text working in 2d slice windows (H)<br />
* Set one time place as the default in the annotation module (add a persistent radio button?) (H)<br />
* Rulers <br />
** expose the tick mark options in the GUI (need to support mice, humans, galaxies) (L)<br />
** use the NeuroDTI example data set from Ron's drop box (H)<br />
** 3d tumor model when measuring it's diameter, the measurement text is hidden inside of it, add an option to position the text at and end or in the middle (L)<br />
** toggle label visibility (M)<br />
* Bidim <br />
** does RECIST need to be orthogonal? Yes<br />
** add the word orthogonal to the tooltip (done)<br />
** make a new icon with a quarter circle between two arms of the axes and use it (???)<br />
* Reformat widget <br />
** estimated time to implementation? (email sent to Will S.) <br />
* Save <br />
** Ron vetoed the Save panel in the Annotation module, all saving is to be done via the centralised widget (???)<br />
** take out the save/load buttons, move the report buttons to another part of the GUI (??)<br />
** add the screen snapshot functionality (especially the over sampling) to the scene views pop up window and bring it up from the shortcut box in the lower left of the GUI (this may need some infrastructure changes) (M)<br />
* Workflows <br />
** use the DTI Tumor scene as a sample (M)<br />
** when Ron created the views, each scene view is a workflow end point (???)<br />
** once the annotation functionality is all there, Nicole will meet with Ron and add the annotations to the scene view and save a new scene, and also document the process for usability improvements and testing (M)<br />
* ROIs<br />
** see the Slicer3 crop volume module for a good initialization method: make the ROI node and then update it by clicking in the 2d slice (M)<br />
** 2d annotation ROI -> label map (H)<br />
** match handle colours of the widget to 2d elements in the GUI (H)<br />
** implement the fit ROI to volume functionality (???)<br />
* Scene views (M)<br />
** test the Neuro DTI file on Slicer4 <br />
** create a new Slicer4 Annotation Testing mrml file and upload it to the drop box<br />
<br />
= Display Properties of Widgets =<br />
* Unavailable / Unknown:<br />
** Set text colors for Ruler and Angle Widget <br />
** Get/Set glyph scale / point size for point display node<br />
** Get/Set text opacity/ambient/diffuse/specular from text display node <br />
** Color of "angle line" cannot be defined <br />
* Available:<br />
** Get/Set text colors from display node<br />
** Get/Set text scale from display node<br />
** Get/Set point colors from point display node<br />
** Get/Set point opacity/ambient/diffuse/specular from point display node<br />
** Get/Set line colors from line display node<br />
** Get/Set line width/opacity/ambient/diffuse/specular from line display node<br />
** Get text format for angle and ruler</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation&diff=67133Projects:ARRA:miAnnotation2011-05-13T15:10:58Z<p>Pohl: /* Meeting with Ron 05/06/11 */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
<br />
= Aim =<br />
[[Image:SlicerAM_QtAnnotation.png|241px|right|Annotation Module]]<br />
<br />
Medical images often contain a wealth of information, such as anatomy and pathology, not explicitly accessible. One way to address this issue is via image annotation and markup. We propose to create a comprehensive framework for annotation and markup within 3D Slicer, enabling users to capture structured information easily. Furthermore, we will develop schemas for saving and recovering this information into and from XNAT, allowing queries of larger data sets of medical scans. This tool will provide clinicians with a relatively simple way to capture information latent in medical scans, and also to select micro-cohorts of medical scans for studying diseases.<br />
<br />
= Research Plan =<br />
3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include: <br />
* a rich set of geometric objects for improved visual differentiation between annotations<br />
* markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection<br />
* entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologiesand <br />
* a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT.<br />
<br />
We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region.<br />
<br />
The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values. <br />
<br />
Both modules are accompanied by training materials and documentation to ensure usability.<br />
=Design of Module=<br />
* Current [[Media:AMI-GUI-Design.ppt | GUI ]] outline - [[Media:SlicerAM QtAnnotation.png | Screenhot]] in Slicer <br />
* Suggested [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] outline<br />
* Wendy's Mouse Mode sketches http://www.slicer.org/slicerWiki/index.php/Slicer4:UIDesign:MouseModeSketches<br />
<br />
= Documentation=<br />
* [[ miAnnotation_Documentation | Documentation ]] of the module<br />
* Using the [[Media:Slicer4_miAnnotation.ppt | module]] with corresponding data ([[Media:Slicer4_miAnnotation_data.zip | sample data]] )<br />
<br />
=Key Personnel=<br />
10% Kilian Pohl (UPenn) <BR><br />
95% Daniel Haehn (UPenn) <BR><br />
5% Dominique Belhachemi (UPenn) <BR><br />
<br />
=Past Contributors=<br />
Yong Zhang (IBM) <br><br />
<br />
=Events=<br />
* 05/18/10 [[Media:miAnnotation_May2010_Yong.pdf | Presentation]] at the Department of Healthcare Informatics, IBM, Almaden<br />
* 12/16/09 - 12/17/09 [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]]<br />
* 01/06/10 [[AHM2010:AnnotationBreakout | Break out session]] at AHM 2010<br />
* 01/19/10 Biweekly Annotation Tcon from 4:00 - 5:00 pm EST (next meeting 2/9): Tel: (218) 862-1115 Conference ID: 348265#, [https://www.lotuslive.com/join?schedid=4572317 Desktop Sharing ]<br />
* 08/30/10 Budget Year 1 [[ Projects:ARRA:SlicerAM:Meeting20100831 | Review meeting ]]<br />
<br />
=Progress=<br />
* 06/05/11<br />
** fiducials are now shows the same way in 2D and 3D<br />
** the property dialog is connected to configure point colors and glyph types for fiducials<br />
** it is possible to add text to a fiducial in 3D<br />
** meeting with Ron to discuss further development and usability issues<br />
* 04/29/11<br />
** fixed the flickering when placing or interacting with fiducials and rulers<br />
** removed some obsolete render calls to enhance performance<br />
* 04/22/11<br />
** worked together with Nicole<br />
*** finally fixed the crash on Slicer exit<br />
*** investigated why MRMLScene import works fine with the annotations but MRMLScene load does not<br />
**** first success: import and load mrml scenes now both load the annotations in 2D and 3D<br />
* 04/15/11<br />
** Maintenance<br />
* 04/08/11<br />
** Maintenance<br />
* 04/01/11<br />
** Maintenance<br />
* 03/25/11<br />
** Maintenance<br />
* 03/18/11<br />
** Work on MRML Load/Save issues (Nicole)<br />
** Maintenance<br />
* 03/11/11<br />
** Work on hierarchies (Nicole)<br />
** Maintenance<br />
* 03/04/11<br />
** Maintenance<br />
* 02/25/11<br />
** Maintenance<br />
* 02/18/11<br />
** Maintenance<br />
** Communication with Daniel Rubin from Stanford to plan AIM integration<br />
*** provided Annotation MRML examples<br />
* 02/11/11<br />
** Maintenance<br />
* 02/04/11<br />
** Clarified how to add Node Selectors for Annotations to the GUI of 3rd Party 3D Slicer Modules<br />
*** Kitware provided necessary infrastructure<br />
*** Proof of Concept in the new CropVolume module with ROI Annotations (Andriy)<br />
** Clearing up the Annotation Storage Node Tests (Nicole)<br />
* 01/28/11<br />
** Presented Annotation module and SceneView module at NAC EAB Meeting<br />
** Smaller bugs and maintenance<br />
** Meeting with Nicole and Alex concerning the final API of hierarchies in Slicer4<br />
* 01/21/11<br />
** Re-activated ROI annotation with backwards compatibility to the old vtkMRMLROINode<br />
*** Tested successfully with a scene from Slicer3<br />
*** Provided documentation to relevant people<br />
** Rulers now support the measurement tape behavior<br />
** Changed the UPenn logo<br />
** Several smaller fixes<br />
** provided Wendy with Screenshots for NAC Poster<br />
*** [[File:Annotation.png|none|thumb|The current state of the Annotation module.]]<br />
*** [[File:Report.png|none|thumb|The report dialog.]]<br />
** Found displayableManager inconsistency between 2D and 3D and the MRML Node Added Event<br />
** MRML backwards compatibility fix for all Annotations<br />
*** new tag "visible", old tag "visibility"<br />
* 01/14/11<br />
** Attended NA-MIC project week<br />
**Enabled picking when placing annotations in 3D. <br />
**Fixed display of ruler intersections. <br />
**Added new icons. <br />
**Use only three seeds to place bidimensional widgets which results in more stability. <br />
**It is also now possible to add annotations to the toplevel hierarchy after another hierarchy was created by clicking in an empty space of the treeView.<br />
**Re-added the ROI functionality, so now we have 5 widgets<br />
**Ruler: enabled display of ticks (measuring tape mode) in 2D and 3D<br />
* 01/07/11<br />
** re-factored the annotation module in terms of changes in the Slicer4 environment<br />
*** ready for the new developer release<br />
** worked on the outsourced SceneView functionality to make SceneViews survive round-trips (mrml load and save)<br />
* 12/31/10<br />
** Maintenance<br />
** Documentation<br />
* 12/24/10<br />
** Maintenance<br />
** Received the first bug reports of potential users<br />
*** Updated bugtracker<br />
* 12/17/10<br />
** Extended Report functionality<br />
*** now includes screenshots<br />
*** shows the hierarchies<br />
** Sorting of Annotations now possible<br />
** Widgets:<br />
*** added the 3D representation of rulers<br />
*** removed the vtkInteractorRecorder hack by placing the widgets programmatically<br />
** Outsourced the former integrated scene snapshot functionality<br />
*** Wrote a new module called SceneViews<br />
*** vtkMRMLSceneViewNode replaces the old snapshot node and includes thumbnail, description..<br />
**** is not part of the displayable framework anymore<br />
** Added confirmation questions prior to removing annotations<br />
** Worked on MRML save/load<br />
** Updated the priority list: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
** Added a section for known issues: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation#Known_issues<br />
** Annotation module Lines of Code (without .ui files and no blank lines): 24820<br />
* 12/10/10<br />
** Changed some things in the MRML architecture to enhance encapsulation<br />
*** Adding new Annotations should be easier now<br />
** Lock selected, toggle visibility of selected and delete selected implemented<br />
** Report functionality works again<br />
*** Added support to print and export as a HTML report<br />
* 12/03/10<br />
** Added icons to the hierarchy tree<br />
** Configured a proxy model to display only vtkMRMLAnnotationHierarchyNodes and vtkMRMLAnnotationNodes in the hierarchy tree<br />
** Smaller layout fixes<br />
** Added 'full layout' thumbnail functionality to Annotation snapshots<br />
** Removed the old table and replaced fully by the treeView<br />
** Over 1000 of lines of code were removed<br />
*** Hierarchies are now usable<br />
*** [[File:Annotationscreenshot.png|none|thumb|Screenshot of an example Annotation using the new features]]<br />
* 11/26/10<br />
** Added functionality to the module logic to be able to place fiducials programmatically<br />
*** This will be used if one presses the 'p' key on a slice view<br />
** Re-activated the text annotation<br />
*** Used vtkCaptionWidget instead vtkTextWidget to be able to have an anchorpoint in 3D space<br />
** The scene, camera and view nodes are now hidden from the hierarchy tree<br />
*** The toplevel annotation hierarchy is the new root and also hidden<br />
** Added functionality to show Annotation snapshot nodes in the hierarchy tree<br />
*** This required adding the original snapshot node to the displayable framework (as a workaround)<br />
*** Later, we will add thumbnail and description directly to vtkMRMLNode, so that a screenshot can be attached to every MRML node<br />
** Overall code polishing in terms of code conventions<br />
*** including the destruction of the frozen seedWidget on Slicer exit<br />
* 11/19/10<br />
** Small fixes to the Annotation snapshot functionality<br />
** New functionality: reset view to when the annotation was placed<br />
** Derived qMRMLAnnotationTreeWidget and qMRMLSceneAnnotationModel to support hierarchies in the module<br />
*** the widgets let us customize the look and feel of the treeWidget<br />
*** in this context, fixed the creation of hierarchies to a specific order in the scene (which is need for the widget)<br />
*** the Annotation hierarchy nodes and the Annotations get already displayed in the treeWidget<br />
** Fixed stack smashing in connection with a recently introduced compiler flag<br />
* 11/12/10<br />
** All widgets are now restricted to the current renderer which makes the interaction more robust.<br />
** Fixed funky behavior after fiducials were placed.<br />
** New functionality: Annotation snapshots (screenshot + description + scene snapshot) implemented.<br />
*** [[File:snapshot1.png|none|thumb|The new annotation snapshot functionality (part 1)]] [[File:snapshot2.png|none|thumb|The new annotation snapshot functionality (part 2)]]<br />
* 11/05/10<br />
** Widget Design Fiesta http://www.na-mic.org/Wiki/index.php/WidgetDesign2010<br />
** Widget intersections works nearly perfectly<br />
*** Unfortunately, only for centered datasets<br />
** Restrict ruler placement to the current renderer works now. This means, the ruler does not disappear when one point moves outside the sliceview.<br />
* 10/29/10<br />
** Lightbox view works for Fiducials<br />
*** Other widgets have to be refined to be used in a lightbox view due to inconsistent VTK API. The VTK Widget Fiesta should target this.<br />
** Widget intersections in the works, not perfectly working yet.<br />
* 10/22/10<br />
** Priority list for the December release of Slicer4: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
* 10/15/10<br />
** Adopting the old TCL logic to enable 2D widgets on reformats and lightbox views<br />
*** Still working on the lightbox view (very close)<br />
* 10/08/10<br />
** Code-cleanup of the logic class - any old and clumsy code was removed.<br />
** Introducing the StringHolder design pattern [(c) Steve] to always show measurement correctly in the GUI.<br />
** Widget creation now works on Unix aswell.<br />
** Added the RegisterNodes method to register node classes when the scene gets attached to the logic class.<br />
** Hierarchy nodes get added when an annotation is created (code workflow to be optimized).<br />
** Configured a nightly build system to build and test the annotation code every night on a SPL workstation.<br />
* 10/01/10<br />
** The hierarchy changes will replace the table in the GUI with a tree widget<br />
*** Added a tree widget to the GUI additionally to the table to display both during the transition stage<br />
** Fixed the follower bug, which sometimes dragged the second controlpoint of a widget behind when the other controlpoint was moved.<br />
* 9/24/10<br />
** Wrote performance test for vtkWidgets in a standalone VTK mode<br />
*** compared performance in Slicer against standalone VTK<br />
*** rendering of text labels was found to be the performance hog, disabling these labels increases performance inside and outside Slicer dramatically<br />
** Meeting between Wendy, Nicole, Steve and Daniel to review the Annotation module status<br />
*** Notes: [[Projects:ARRA:SlicerAM:Meeting20100921]]<br />
** Annotation hierarchy in the works<br />
* 9/17/10<br />
** 2D placement of Rulers, Bidimensional and Fiducials works now<br />
*** The widgets get synchronized along the slice viewers and the 3D view<br />
** Added extra layer on top of vtkWidgets and vtkWidgetRepresentations to add some extra functionality like calculating distances of measurement correctly in 2D<br />
*** bidimensional measurement and rulers now show the correct distance also in 2D<br />
** Fixed possible null pointer exception in vtkMRMLSliceLogic<br />
** Refactored GetSliceOffSet from vtkMRMLSliceLogic to vtkMRMLSliceNode<br />
* 9/10/10<br />
** 2D placement of Annotations in the works<br />
*** change of the underlying architecture to use one displayableManager for 2D and 3D resulting in less code duplication<br />
*** to perform the changes, all annotations but fiducials were disabled for now<br />
* 9/3/10<br />
** Annotation module status review and planning meeting took place in 1249 Boylston<br />
*** Agenda and Notes: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:Meeting20100831<br />
**** includes new generated class diagram<br />
** Property dialog updated (see screenshot)<br />
*** [[File:Annotationpropertydialog.png|none|thumb|The new annotation property dialog.]]<br />
*** first MRML-Widget synchronization works, the text tab in the property dialog works well with the text widget<br />
** new icons for bidimensional measurement and ROI by Wendy<br />
** updated ctkColorPickerButton to include the ability to disable the setting of the color hexcode as the buttontext to avoid the workaround we had in the annotation module<br />
* 08/27/10<br />
** added a work-around to initialize renderer properly resulting in improved display of annotations in 3D viewer<br />
** cleaned up the code (more then 1000 lines of code where obsolete)<br />
** updating property dialog, which includes revisiting the displayableManagers to support MRML and widget updates<br />
* 08/20/10<br />
** fiducials and sticky node work now<br />
** ruler and spline work now<br />
*** spline widget causes problems b/c after one spline was placed, no interaction with 3D scene possible<br />
** ROI works now<br />
** all annotations now can be placed to examine widget behavior<br />
** started working on a new interface for the property dialog<br />
** consolidated experts for 2D slice displayableManagers<br />
** started working on synchronizing the widgets with MRML display nodes<br />
** fixed GUI problem: the table did not expand even if there was free space in the module frame. now it works.<br />
* 08/13/10<br />
** Wendy, Nicole and Daniel discussed how to integrate mouse modes of Slicer into Annotation module and vice versa. Solution is a widget which appears in the Annotation module panel but can also be shown outside of it as a toplevel window in Slicer (maybe with keybinding), see here: http://wiki.na-mic.org/Wiki/index.php/File:Widget.png<br />
** current status (workflow, user places seeds and widget appears):<br />
*** angle annotations work (note: the widget did not support programmatical placement. a trick is used to place the widget where the user has clicked)<br />
*** text annotations work<br />
** modified vtkMRMLInteractionNode to have a customTag for place modes not only from annotation module but all modules<br />
* 08/06/10<br />
** Enhanced the workflow for creating text annotations. This approach should serve as a general framework for all annotations (sequence diagram available http://wiki.na-mic.org/Wiki/index.php/File:TextAnnotationWorkflow.png)<br />
** modified vtkMRMLInteractionNode to support the place modes for the annotations<br />
*** meet with Wendy next week to discuss integration<br />
** added a click counter class to support the creation of widgets with multiple clicks (very generalized to support all annotations)<br />
*** plan is to place seeds before the actual widget gets created<br />
* 07/29/10<br />
** Created an extra layer called vtkMRMLAnnotationDisplayableManager which serves as a superclass for all specific Annotation displayableManagers. F.e. the vtkMRMLAnnotationTextDisplayableManager is now really lightweight.<br />
** Coordinated with Wendy to add additions interaction modes to vtkMRMLInteractionNode to support different interaction types for different annotations. This will happen under the hood, so the user sees only the "place" mode.<br />
** Got together with members of the 3D & Advanced Imaging Lab at UPENN to investigate how commercial products realize annotations (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:vtkWidgets#How_do_they_do_it.3F).<br />
** Interactive placement of text annotations is now possible. This should be the standard way of placing annotations for all available types.<br />
** Added a test for the creation of a text annotation and its widget without a displayableManager (vtkMRMLAnnotationTextNodeAndWidgetTest1)<br />
** Removed initial values from AnnotationNodes due to different seg-fault errors when properties where not initialized. To cut down confusion, no initializations are now necessary.<br />
* 07/22/10 <br />
** Meeting of Nicole, Steve and Daniel to talk about architecture<br />
*** biggest change is the introduction of a hierarchy for annotation<br />
**** more information and discussion during the tcon:[[Projects:ARRA:miAnnotation_Meeting_07202010|Meeting / Weekly meeting]]<br />
** fixed AnnotationTextDisplayableManager to support multiple text annotations<br />
** added a test for the AnnotationTextDisplayableManager<br />
** property dialog for annotations gets displayed again, nevertheless the connection to the MRML display nodes needs further work<br />
* 07/15/10<br />
** add text nodes using the new displayable manager architecture is now possible<br />
*** nevertheless, full functionality is not restored yet<br />
** added fiducial displayable manager<br />
** new Slicer bug tracker category: Annotations<br />
*** filed open bugs and feature requests - please add all new requests there<br />
* 07/08/10<br />
** moved tests to Testing/Cxx<br />
** created a superclass for all displayable managers (vtkMRMLAnnotationDisplayableManager)<br />
** created vtkMRMLAnnotationTextDisplayableManager based on the old qMRMLAnnotationTextManager<br />
** working on the add text node functionality with the new displayable manager<br />
** fixed linking errors appearing on the Slicer Dashboard<br />
* 07/01/10<br />
** re-factored module from miAnnotation to Annotation<br />
** re-integrating functionality without KWWidgets<br />
*** MRMLDisplayableManager was created by Kitware guys and includes base functionality for the re-integration<br />
*** starting with adding text nodes<br />
**** UML diagram for involved classes: [[MiAnnotation_Documentation#Development]] (needs to be checked for logic/manager/mrml pattern consistency) <br />
** added option to set helptext for the module in consistency with qSlicerWidget<br />
* 06/24/10<br />
** Compiling without KWWidgets on Mac OS is now possible.<br />
** Starting to include the functionality of KWWidgets in pure QT code.<br />
** Daniel Haehn took over project from Yong Zhang.<br />
* 06/18/10<br />
** Tutorial is created.<br />
** GetAnnotationMeasurement is modified to return multiple measurements.<br />
** ROI annotation is modified to display extension measurements.<br />
** Bidimensional annotation is modified to display bi-line measurements.<br />
* 06/11/10<br />
** Documentation page is created.<br />
** Bugs for property dialog are fixed.<br />
** Constructions of Bidimensional and Spline annotations are modified using proper control point initialization.<br />
** Bugs for showing values for some annotation types are fixed. <br />
* 06/04/10<br />
** vtkSlicerAnnotationROIManager is implemented.<br />
** vtkSlicerAnnotationTextManager is implemented.<br />
** vtkSlicerAnnotationSplineManager is implemented.<br />
** vtkSlicerAnnotationBidimensionalManager is implemented.<br />
* 05/28/10<br />
** vtkMRMLAnnotationROINode is added;<br />
** vtkMRMLAnnotationBiDimensionalNode is added;<br />
** vtkMRMLAnnotationSplineNode is added.<br />
** Logic and ModuleWidget are modified to include new Nodes<br />
* 05/21/10<br />
** ROI, Text, BiDimensional, and Spline Annotations are initialized.<br />
** fixed BUG: HTML report cannot be saved properly.<br />
* 05/14/10<br />
** fixed BUG: When opening display properties from Sticky note -> reduce frame and enlarge it again by pressing triangle next to title : value and coordinates appear<br />
** fixed BUG: fiducial manager is added.<br />
** fixed BUG: AnnotationMouseModePick/Place are updated.<br />
* 05/07/10<br />
** fixed BUG: Lock does not lock the position of a widget in the 3D Viewer<br />
** fixed BUG: changing coordinates to AngleNode does not have any effects on the Angle Widget.<br />
** fixed BUG: fix coloring for annotation selection<br />
*04/30/10<br />
** fixed BUG: changing control points cannot be done when property dialog is open.<br />
** fixed BUG: annotation is not highlighted when selected.<br />
** fixed BUG: starting from the 2nd annotation, changing the location of the left point for ruler or center point for angle does not update the table properly.<br />
** fixed Bug : changing the center point of angle node does not update table properly<br />
* 04/23/10<br />
** Created a ruler widget manager <br />
* 04/16/10<br />
** Created the new annotation type sticky note, which allows you to enter text independent from the viewer<br />
* 04/09/10<br />
** Modified source code to be compliant with VTK 5.6<br />
** Grid out your buttons (Create Frame)<br />
** Fixed BUG: When changing line color in Display Properties it changes the Text Color<br />
** Added script for testing color setting <br />
** Fixed BUG: Label of line color changes in property window when defining a unselected color<br />
<br />
* 04/02/10<br />
** Fixed BUG: Nothing happens when Property Window is open and you press the edit button for another annotation<br />
** Restructured Annotation MRML<br />
** Fixed Bug: Resetting of Lines and Points does not work correctly GetNumberOfLines > 0 <br />
<br />
* 03/26/10<br />
** The property restoration is now implemented properly.<br />
** Property Modification is re-designed to simplify the operation.<br />
** Removed bug: ruler/angle disappear after adding fiducials <br />
** Removed BUG: in property dialog, when editing the text, the character is entered from right to left.<br />
** include lock annotation into option button (use same logic as for new (De)select All button)<br />
** For each annotation type provide list outlining which display property can be changed, which cannot , and which one you do not know <br />
** Resolved BUG: When saving a report with a file name that already exists then the following message appears in the command shell "Error: cannot make directory" and directory with files is not updated<br />
** Resolved BUG: Annotation Properties: (Un)selected color is initially white even though widget in 3D viewer is different<br />
** Resolved BUG: Select Color window does not show the correct color<br />
** Resolved BUG: Selected and Unselected Color are switched<br />
** Define Tooltips for fiducial, angle, ruler,report, save mrml button<br />
** In table: Add proper tool tip for visualization and edit button<br />
** Resolved BUG: when saving report with out ending html to the file name - icons will not be saved under Linux<br />
** Created Test Module for testing miAnnotation logic<br />
** In collaboration with Nicole Aucoin figured out line display bug in 3D Viewer <br />
** Use the Kitware slider and colorPicker under Display Property<br />
** Fixed BUG: Slicer crashes when creating an annotation while Display properties is open, and when closing the property window and then pressing edit for the new annotation<br />
<br />
* 03/19/10<br />
** In the property window display properties are shown via collapsed frame by default<br />
** List all attributes for text/point/line and implement those that can be modified<br />
** Fixed BUG: When pressing the property button warning messages pop up in my command shell <br />
** Annotation Properties: For Angle and Ruler Widget also shows now values of AnnotationDisplayNode and AnnotationControlPointsNode<br />
** Change design of html report <br />
** Implemented text edition and update for ruler and angle widgets.<br />
** Changed the default mouse mode icon to MousePick.<br />
** Modified Report Dialog to avoid horizontal slider when screen shot is included in the report.<br />
** Removed multiple warning messages.<br />
** Fixed Bug in Report: empty text fields are displayed without boundaries <br />
** Ruler Distance is now displayed just in mm <br />
** After talking to BWH changed name of tool from Reporting to miAnnotation<br />
* 03/12/10<br />
** Created icons for:<br />
*** edit conditioning for all annotation types (done), <br />
*** mouse mode icons, pause, play, cancel, ok/done, (Un)lock (done)<br />
*** new the annotation types poly line, spline with control points, volume information extractor, and sticky note (done)<br />
*** Modify fiducial icon just to show one star and change save annotation icon (done)<br />
*** Modify save annotation and save scene icons (done)<br />
*** Modify move up/down delete icons (done)<br />
** Write 5 page, double column, AMIA paper about Reporting<br />
* 03/05/10<br />
** Removed Warning Messages when compiling<br />
** Fixed Bug: When entering text in property box (under linux) it is entered from right to left instead left to right <br />
** Fixed Bug: Annotation Property: funny behavior with selecting set of digits in a numerical value and typing in a numeric value - only the first digit gets change.<br />
** Fixed Bug: Value of Angle node is not update in table<br />
** Fixed Bug: Updating the value in the table slows down the operations<br />
** Changed the default ruler from 1mm to 500mm.<br />
** Angle Widget is added by manually clicking three points on the viewer. The angle value is now shown in the table. The behavior of the angle button is in the "toggle down" state until all three control points are set<br />
** When selecting annotation in table, color of annotation in 3D Viewer changes to selected color <br />
** Revised "add ruler" button to click-style instead of toggle-style<br />
** When creating a new annotation, set this entry to selected and all other table entries to unselected<br />
** (De) Select All button: change as discussed with Wendy Plesniak, BWH, to option button with proper logic<br />
** Setting color/selected color for individual Ruler and Angle widgets in property dialog<br />
** Fixed Bug: hiding/unhiding ruler and angle annotations<br />
** Change display property for each annotation individually<br />
** Lots of warning messages when compiling code<br />
* 02/26/10<br />
** Created pop up window showing screen shot<br />
** Manual editing of coordinates via "Property Window"<br />
** Resolved column width problem in table ([http://wiki.na-mic.org/Wiki/index.php/File:Screenshot-Form.JPG original problem], [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_TableV2.png second screen shot problem])<br />
** Fixed bug where hide icon changed size in table<br />
** Include icons when saving html report in a directory with the same name as the html file<br />
** [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_GUI.png Reorganized GUI] based on feedback from Wendy Plesniak, BWH <br />
** Include screen shots (if any) in the report (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_ReportV1.png an example])<br />
** Fixed the following bug: After resizing the 3D Window taking a screen shot only displays the window with the original size (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Window.png screen shot]) <br />
** Fixed Bug: Value update of ruler widget is slow <br />
** Text defined in property box now shows up in table<br />
** Integrated vtkMRMLAnnotationAngleNode with AngleWidget<br />
** Added new buttons to create frame based on feedback from BWH <br />
* 02/19/10 <br />
** Implement a general structure for vtkMRMLAnnotation*Node<br />
** Work together with Kitware to resolve QT Table layout problem <br />
** Allow defining long text annotations for each widget<br />
** Improve user interaction through pop up windows when trying to modify an existing annotation <br />
** Creating and removing ruler now works correctly <br />
** Use correct label format to display measurement values in Annotation Property window <br />
** Created a "Save annotation" Window<br />
** Fixed changing icon size in table (see original [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Table-IconProblem.png screen shot] )<br />
** Fixed slicer crashing closing the property window <br />
** Renamed and resized columns in Table<br />
*02/12/10 removed bugs related to table buttons, linked button to angle widget and ruler widget<br />
*02/05/10 implemented "Save Annotation Report" button and "Move up/down" buttons; added extra column in the report table for visibility; modified annotation property dialog; implemented button-click in the table.<br />
*01/29/10 implemented functionality for "Annotation Property Modification" button, "Create Report" button, and integrated new icons for buttons.<br />
*01/22/10 Set up the source control for the reporting module; implemented functionality for "Select All" button, "Visible" button, and "Delete" button in the GUI; created new icons for buttons<br />
*01/15/10 Organized biweekly Tcon <br />
*01/08/10 Participated in all week All Hands Meeting in Utah; Expanded QT interface with functionality to set seeds in images; Defined a final MRML Structure for storing annotation. <br />
*01/01/10 Generated a [[Media:SlicerAM QtAnnotation.png | GUI interface]] via QT for the annotation module. [[Projects:ARRA:SlicerAM#Widget_related_action_items | Reviewed ]] all VTK Widgets related to annotation. <br />
*12/25/09 Created [[ 2010_Winter_Project_Week_mComment | project ]] and organized [[ AHM2010:AnnotationBreakout | break out session ]] at AHM meeting. Coordinated efforts with BWH team in preparation of the meeting. <br />
*12/18/09 Held workshop to integrate AMI into 3D Slicer. Hired new person to implement AMI in Slicer. <br />
*12/11/09 [[ Projects:ARRA:SlicerAM_RSNA09Report | Summary ]] of tools demoed at RSNA <br />
*12/04/09 Visited RSNA to review annotation tools by GE, Siemens & Phillips. Connected to caBIG AIM project to see how we can make use of their data scheme <br />
*11/29/09 Created GUI for MarkUp module <br />
*11/20/09 Design MRML Structure of Annotation and MarkUp Module<br />
*11/13/09 Organize [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]] Session<br />
*11/06/09 Designed User Interface , Meet with Julien Finet and Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Participated in Qt-Tcon, Interviewed candidate at Almaden, coordinated efforts with Nicole Aucoin <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<br />
<br />
= Feature Request =<br />
== VTK Widgets ==<br />
* For further detail go [[ Projects:ARRA:SlicerAM:KWWidgets | here ]]<br />
<br />
== QT Related ==<br />
* Submit bugs and feature request via [http://na-mic.org/Mantis/search.php?project_id=1&category=QtGUI&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 Mantis]<br />
* Feature requests that may open discussions can be added [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/OpenDiscussions here]<br />
<br />
== Daniel ==<br />
All features/issues are listed here: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList<br />
=== Known issues ===<br />
* MRML<br />
** <strike>After loading of scene, the annotations are not displayed in the hierarchy tree anymore</strike><br />
** Load scene does not display 3D widgets, Import scene does<br />
** After importing or load, the user has to click on the widget to enable the connection between tree entry and widget<br />
* Annotations<br />
** Property dialog does not work yet and might crash<br />
** Pick mode does not work correctly, if placement was paused and resumed (the first picked coordinate gets lost)<br />
** <strike>Screenshot imagedata does not get saved on Scene save</strike><br />
* GUI<br />
** if moving an annotation up or down inside a hierarchy, the tree gets confused<br />
** Drag and drop does not work<br />
** <strike>after creating hierarchies, the selected item does not reflect the hierarchy which new annotations get added to</strike><br />
** save buttons not implemented<br />
** <strike>widget intersections do not work</strike><br />
** <strike>Slicer4 crashes on exit after annotations were placed and the scene was not closed manually prior exiting Slicer</strike><br />
<br />
==== Feedback by Users ====<br />
* Ron<br />
<pre><br />
1. I sometime like the fiducials to be spheres, not crosses. In Slicer 3 we had a whole list of options. Can I have them for Slicer4? Can I also change their size?<br />
2. The ruler has different colors in the 3D view and in the slice views. That is wrong.<br />
3. The properties popup require a lot of clicking, including double click. Usability will need to be optimized.<br />
4. No drag and drop in the module.<br />
5. text annotation: arrow in the slice view, but not in the 3d view (see attached)<br />
6. text is not in the box in the slice view<br />
7. the font is butt-ugly. In addition, part of the letter n is cut off by the t. The space between the capital V and the e is too big<br />
8. Slicer 3 let you jump to a fiducial location by right clicking in the list in the module.<br />
9. Also, The ruler does have issues with visibility, when the slice is rendered as well. See attached screensnapshot: little dots to the left, no dots to the right.<br />
</pre><br />
* Isaiah<br />
<pre><br />
1) need "selected" parameter for each fiducial, separate from visibility. It's used as boolean inclusion criteria in several modules - in my case DTI FiducialSeeding but also some other ones like segmentation and for CLI modules.<br />
2) need to set properties for groups of fiducials at once. This is tricky because the hierarchy is generic, but ability to set all parameters for a group of fiducials in one place is important.<br />
3) meta visibility control is helpful but maybe not imperative, ie show/hide a whole group but still maintain the individual visibility settings.<br />
4) flicker of fiducials in 2d-view slice whenever other fiducial is moved across that slice. I have two coplanar fiducials in coronal slice, and move a third back/forth across the axial slice. Each time the third crosses the coronal there is a noticeable flicker of the two fiducials in-plane.<br />
5) positioning with decimal precision rather than integer?<br />
6) the persistent-drag mouse interaction in both 2d and 3d is not ideal (at least to me).<br />
7) deleting a hierarchy with ~30 fiducials incurs a noticeable delay around 7s. I compiled with the standard (debug mode?) instructions on x86, ubuntu 10.04.<br />
8) there are some strange mouse interactions when placing in the 3d view after clicking the "cancel" or "accept" buttons. for example, the first time I create a list it works fine: one click to place each. However, if I stop, delete, and start adding again then it doesn't work the same way: the first click makes a fiducial, but subsequent clicks only occasionally place new fidus. I think the problem is that the interactor is selecting the new first fiducial even if the mouse is very far away - can click on the other side of the screen and drag that fiducial, even after pressing "stop" again.<br />
8a) minor style: is it possible to use stop-sign or something else rather than the current x-in-circle for "cancel"?... my brain sees that as the fiducial button 1/2 the time :)<br />
9) I'm confused by the edit properties display (window) for fiducials. What is the purpose for each tab: text, points, lines? points seems to be a place for a list, but x/y/z is empty and position is instead displayed under "Measurement value" on the text tab.<br />
</pre><br />
<br />
==== Meeting with Ron 05/06/11 ====<br />
Nicole and Daniel met with Ron to discuss usability issues and future development.<br />
<br />
<br />
* Ron would like the 3d sphere to be the default setting for the glyphs. (A)<br />
* Change the mouse cursor when in place mode, use the images from the mouse modes toolbar icons. (B)<br />
* Text annotations (C)<br />
** line breaks for long text, automatic (C.1)<br />
** show some of the text (first 20chars?) in the fiducial text box with ... to denote more visible in the Qt interface (C.2)<br />
** sometimes don't want an arrow head (C.3)<br />
** consolidate the text and fiducials into one conceptual package allowing turning on/off the text box, detaching it, leader, etc. (C.4)<br />
** get the text working in 2d slice windows (C.5)<br />
* Set one time place as the default in the annotation module (add a persistent radio button?) (D)<br />
* Rulers (E)<br />
** expose the tick mark options in the GUI (need to support mice, humans, galaxies) (E.1)<br />
** use the NeuroDTI example data set from Ron's drop box (E.2)<br />
** 3d tumor model when measuring it's diameter, the measurement text is hidden inside of it, add an option to position the text at and end or in the middle (E.3)<br />
** toggle label visibility (E.4)<br />
* Bidim (F) <br />
** does RECIST need to be orthogonal? (F.1)<br />
** add the word orthogonal to the tooltip (done)<br />
** make a new icon with a quarter circle between two arms of the axes and use it (F.2)<br />
* Reformat widget (G) <br />
** estimated time to implementation? (email sent to Will S.) (G.1)<br />
* Save (H)<br />
** Ron vetoed the Save panel in the Annotation module, all saving is to be done via the centralised widget (H.1)<br />
** take out the save/load buttons, move the report buttons to another part of the GUI (H.2)<br />
** add the screen snapshot functionality (especially the over sampling) to the scene views pop up window and bring it up from the shortcut box in the lower left of the GUI (this may need some infrastructure changes) (H.3)<br />
* Workflows (I)<br />
** use the DTI Tumor scene as a sample (I.1)<br />
** when Ron created the views, each scene view is a workflow end point (I.2)<br />
** once the annotation functionality is all there, Nicole will meet with Ron and add the annotations to the scene view and save a new scene, and also document the process for usability improvements and testing (I.3)<br />
* ROIs<br />
** see the Slicer3 crop volume module for a good initialization method: make the ROI node and then update it by clicking in the 2d slice<br />
** 2d annotation ROI -> label map<br />
** match handle colours of the widget to 2d elements in the GUI<br />
** implement the fit ROI to volume functionality<br />
* Scene views<br />
** test the Neuro DTI file on Slicer4<br />
** create a new Slicer4 Annotation Testing mrml file and upload it to the drop box<br />
<br />
= Display Properties of Widgets =<br />
* Unavailable / Unknown:<br />
** Set text colors for Ruler and Angle Widget <br />
** Get/Set glyph scale / point size for point display node<br />
** Get/Set text opacity/ambient/diffuse/specular from text display node <br />
** Color of "angle line" cannot be defined <br />
* Available:<br />
** Get/Set text colors from display node<br />
** Get/Set text scale from display node<br />
** Get/Set point colors from point display node<br />
** Get/Set point opacity/ambient/diffuse/specular from point display node<br />
** Get/Set line colors from line display node<br />
** Get/Set line width/opacity/ambient/diffuse/specular from line display node<br />
** Get text format for angle and ruler</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=67066Projects:ARRA:SlicerEM2011-05-07T15:20:39Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 05/06/11<br />
** EMSegment3 Updates:<br />
*** New MRI-Human-Brain-Hemisphere task<br />
*** Tested if the GUI produces same results as the command line (for the Human Eye task)<br />
*** New cardiac segmentation task <br />
** EMSegment4 Updates:<br />
*** initialize the AtlasCreatorCxx libraries in the Commandline Tool to be able to use the vtkMRMLAtlasCreatorNode from Tcl<br />
*** worked on using the AtlasCreator python module in the EMSegment Commandline Tool<br />
*** worked on the python-tcl interface for slicer4<br />
*** purged KWLogic class and replaced it with the logic<br />
*** outsourced all Tcl commands in a separate class which is valid for Slicer3 and Slicer4: vtkSlicerCommonInterface<br />
*** switched the EMSegmentCommandline, TclInterpreter, Converter to the new vtkSlicerCommonInterface<br />
** AtlasCreator Updates:<br />
*** added the option to specify the number of Threads<br />
*** in command line: --numberOfThreads X<br />
*** in the GUI: Number of Threads under Misc.<br />
*** if the number of threads are not specified, the AtlasCreator always sets the maximal number of threads for the individual machine<br />
*** setting the cluster mode has no effect on this setting and it will behave the same way (maximal number of threads by default)<br />
*** save the template as template.nrrd insteaf of template..nrrd<br />
* 04/29/11<br />
** EMSegment3 Updates:<br />
*** Added function call to simplify GenericTask.tcl<br />
**** proc CMTKGetPixelTypeFromVolumeNode { volumeNode }<br />
*** Updated HumanEye task<br />
*** Updated CT-Hand-Bone task<br />
*** Updated MRI-Human-Brain task<br />
** EMSegment4 Updates:<br />
*** Adopted the newly available Slicer4 extension infrastructure for the EMSegment4 extension<br />
**** worked together with Kitware on solving issues due to the complexity of our extension (still work in progress)<br />
*** fixed some segfaults and changes in the API (f.e. vtkMRMLAnnotationROINode instead of vtkMRMLROINode, vtkGraph calls etc..)<br />
*** introduced TclConnector which provides an interface to Tcl in Slicer3 and Slicer4 (still work in progress)<br />
** AtlasCreator:<br />
*** disabled tests on Windows in Trunk and Branch<br />
*** modified Wiki page with a hint<br />
*** added feature: show hostname of the head node in the logs<br />
*** fixed bug: use the correct file extension for saving the template<br />
*** fixed bug: don't always use testmode in commandline mode<br />
* 04/22/11<br />
** EMSegment4 Updates:<br />
*** Removed the old versions of the EMSegmenter in Slicer4 since we want to include it now as an extension<br />
*** Created first version of the Slicer4 EMSegment extension, available at a Git repository: https://github.com/haehn/EMSegment4 until the extension infrastructure in Slicer4 is ready<br />
*** The new extension uses the algorithm and logic parts of the Slicer3 module to avoid code duplication and to include all recent changes<br />
*** Modified the Qt GUI to support the new EMSegmenter MRML structure: MRML files from tasks in Slicer3 can now be loaded into Slicer4 to start configuring the GUI<br />
** EMSegment3 Updates:<br />
*** fixed failing test EMSegCL_Task_NonHumanPrimate_BRAINS_small by setting LogCovarianceCorrection="0.01 "<br />
*** fixed failing test EMSegCL_Task_MRIHumanBrainExp_BRAINS_small by setting LogCovarianceCorrection="0.01 0 | 0.01 0 "<br />
*** removed unused label(class) 3 and 7 from Human Eye task<br />
*** applied the Human Eye task on 5 test cases<br />
*** Updated the CT-Hand-Bone task. Replaced the anatomical tree. This task is now using a medical terminology to describes the anatomical tree.<br />
* 04/15/11<br />
**Congealing Updates:<br />
***Created a Slicer extension for the Congealing project based on ( https://github.com/debonet/Congealing )<br />
***The extension is compiling successfully in debug mode on Linux and Mac<br />
**EMSegmenter Updates:<br />
*** Added new task 'Human Eye'<br />
*** Separated EMSegmenter GUI (using KWWidgets) from EMSegmenter base code.<br />
*** Future versions of the EMSegmenter GUI in Slicer4 (using Qt) can be linked against the same base code.<br />
*** Fixed tests<br />
**AtlasCreator Updates:<br />
*** included monitoring mode: ComputeMeanImage-, Registration-, Resampling- and CombineToAtlas-Jobs are now monitored for successful computations. <br />
**** Whenever a failure happens, these jobs get restarted up to 4 times. After that, the Atlas Generation will continue if possible or abort if something required is missing.<br />
*** Added 4 Tests which run on a Nightly base to check if the AtlasCreator is still working.<br />
*** Added version 0.4 to Slicer Trunk and 3.6 Branch<br />
*** Updated the 3.6 Branch Base with necessary recent patches to make the AtlasCreator work<br />
*** Successful manual tests<br />
*** Added Documentation for the Atlas Creator: http://www.slicer.org/slicerWiki/index.php/Modules:AtlasCreator<br />
* 04/08/11<br />
**EMSegmenter Updates:<br />
*** Changed the default colormap to "GenericAnatomyColors.txt"<br />
*** Added new commandline option to switch on/off particular preprocessing steps (--TaskPreProcessingSetting="|C0|C0")<br />
*** Added commandline option (--atlasVolumeFileNames), so we can use the original mrml files, instead of duplicating them<br />
*** Prepared new CMTK extensions for all 3 platforms (Linux,Mac,Windows), compiled in Release mode with platform specific optimization flags. The speed up is 5x-6x<br />
*** Implemented a new task to call the AtlasCreator from within the EMSegmenter <br />
**Atlas Creator Updates:<br />
*** detect labels automatically when using external invocation or the command line tool which was so far only possible in the GUI<br />
*** normalization of atlases does not force the float type anymore<br />
*** finished first version of CongealingCLI wrapper in terms of our un-biased groupwise registration effort and commited it to the Slicer3 trunk<br />
**** created documentation for the wrapper: http://www.slicer.org/slicerWiki/index.php/Modules:AtlasCreator:CongealingCLI<br />
*** added infrastructure to Slicer base to support the Invoke function in connection with KWWidgets<br />
*** handle events in MRML/GUI now properly and loop-safe<br />
*** only create new output folder if the configured one is not empty (now consistent between CLI and GUI)<br />
*** fixed a bug in connection with normalize when using the GUI<br />
*** fixed a possible crash when using the GUI and loading the generated atlases into Slicer<br />
*** added events to the comboboxes and write out MRML on change using the new Invoke method<br />
*** fixed possible memory leaks when using the GUI and exiting Slicer<br />
*** in pair fixed mode, also consider the defaultCase segmentation when combining to an atlas<br />
*** in pair fixed mode, also consider the defaultCase original when generating the normalized IntensityMap of all aligned images<br />
*** fixed possible error when selecting the defaultCase in the GUI: instead of the originals, a segmentation was selected<br />
*** added Testing, for now only a simple vtkMRMLAtlasCreatorNode test<br />
*** also, made sure to copy the TestData to the Slicer3 shared modules directory<br />
* 04/01/11<br />
**Atlas Creator Updates:<br />
*** introduced vtkMRMLAtlasCreatorNode::InitializeByDefault() to set default values to the attributes of the MRML node<br />
*** re-structured the complete Graphical User Interface<br />
**** added events for all GUI elements to store the current state to MRML<br />
*** tested MRML import/load concept with AtlasCreator configurations successfully<br />
*** ran tests on SBIA cluster and identified need of mechanism to restart unsuccessful registration jobs<br />
*** optimized clean-up on Slicer shutdown<br />
*** added infrastructure to the 3D Slicer base to support listening to MRMLScene events without a corresponding calldata like the MRMLClose event<br />
*** PCA Analysis now fully integrated<br />
**** added new options to configure PCA modelling --pcaMaxEigenVectors X and --pcaCombine to the command line tool and the GUI<br />
*** Groupwise Registration effort:<br />
**** hands on Congealing sourcecode and successfully compiled it in different environments<br />
**** analyzed code and defined next steps with collaborators<br />
*** updated http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator#Priority_List<br />
* 03/25/11<br />
**EMSegmenter Updates:<br />
*** The Atlas Creator can now be called from within a tcl script.<br />
*** Added a test script for this kind of invocation<br />
*** The results of the Atlas Creator are now written back to the MRML scene for further processing<br />
*** Performed static code analysis on the EMSegmenter<br />
*** Helped user (WUSTL) to find the optimal setting to segment their MRI data.<br />
*** Restructured the EMSegmenter tests<br />
**Atlas Creator Updates:<br />
*** finished ITK implementation of combineToAtlas step (including normalization, re-casting..) called ACCombiner<br />
*** a lot of bug-fixing, tweaking and performance enhancing<br />
*** replaced the deprecated os.system calls to execute processes by the subprocess methods (new python API)<br />
*** re-structured advanced panel in GUI<br />
*** included PCA analysis capabilities using TCL (80%)<br />
**** available in the command line tool using --pca flag<br />
*** switched the CLI and the logic from the old configuration containers to use the vtkMRMLAtlasCreatorNode<br />
**** it is now possible to configure a MRML Node and invoke a launch event to start an AtlasCreator computation<br />
****also, the API of vtkMRMLAtlasCreatorNode slightly changed to support the NormalizeTo and the DebugMode and DryrunMode settings<br />
*** moved ACCombiner to ACITKTools<br />
**** added new pure ITK tool in ACITKTools, called ACMeanImage to compute a meanImage of a bunch of images<br />
**** edited the AtlasCreator logic to use the ACMeanImage tool instead of computing it in the logic class<br />
**** integrated the ACMeanImage tool in the AtlasCreator cluster API<br />
**** as a result, finally all computation is moved from the headnode in cluster mode, even no images get loaded on the headnode<br />
*** added the feature to return as output as well the normalized intensity maps of aligned cases in dynamic and static mode<br />
*** coordinated effort on integrating Groupwise Registration (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Groupwise)<br />
* 03/18/11<br />
**EMSegmenter Updates:<br />
***ENH: Use Colormap="vtkMRMLColorTableNodeFileSlicer3_2010_Brain_Labels.txt" <br />
***ENH: Update description of preprocessing checkboxes<br />
***BUG: CMTK's registration/warp command cannot change the scalar type of the output volume, resample the atlas in an additional step<br />
***ENH: Adding task for skull stripped brain images<br />
***BUG: (BSplineToDeformationField) Send normal output to stdout instead of stderr , Use 'eval exec ' to execute a command<br />
***BUG: Improve error handling for function calcDFVolumeNode<br />
**Atlas Creator Updates:<br />
*** added fix to perform re-casting only when necessary to enhance performance<br />
*** included distributed computation of the last step: combineToAtlas including re-casting and normalization<br />
**** pure ITK code without XDISPLAY dependency<br />
**** as a result, all computation steps (registration, resampling, combining) now support a cluster environment<br />
*** solved problem of compiling CMTK on SPL cluster<br />
*** added the ability to normalize the atlases to 0..X instead of only 0..1<br />
**** supported in GUI and command line tool<br />
*** added fix to only register/resample images where segmentations exist and vice-versa<br />
*** created proof of concept to run the Atlas Creator from the EMSegmenter using MRML<br />
*** coordinated effort on integrating PCA Analysis (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:PCA)<br />
*** coordinated effort on integrating Groupwise Registration (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Groupwise)<br />
* 03/11/11<br />
**EMSegmenter Updates:<br />
*** Moved IO related functionality into base code<br />
*** ENH: Moved duplicated initialization code into a methed, bumped version number to 3.6.4-beta<br />
*** ENH: pass --fast --verbose options to each CMTK call<br />
*** ENH: Refactoring, move replicated code to new EMSegmentHelper file<br />
*** Adjusted Sandbox so it can use the current EMSegmenterHelper file<br />
*** Investigated a segfault during registration, CMTK's (nrrd reader) couldn't handle uint's , this is now fixed in the newest CMTK<br />
** Atlas Creator Updates:<br />
*** Ran several tests and uploaded the data to http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Tests<br />
*** Identified and fixed problem with CMTK where certain labels were included in other atlases (see URL above, f.e. label 3 and label 9)<br />
*** Commited new version to the Slicer trunk including:<br />
**** Don't use Slicer temp dir anymore, use a temp dir in the output dir instead<br />
**** Refactored cluster mode to be based on a script<br />
**** Cluster script template (template.sh) is configurable for individual needs<br />
**** Added support for CMTK non-rigid registration<br />
**** De-activated multi-threading in cluster-mode for CMTK and BRAINSFit<br />
**** Different wait time for cluster mode for observing finished jobs<br />
**** Added date to print timestamps<br />
**** Distributed computation of Resampling<br />
*** Updated Priority List for new releases on http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator<br />
*** Started working on integrating PCA Analysis (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:PCA)<br />
*** Started effort to include Groupwise Registration (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Groupwise)<br />
* 03/04/11<br />
** Update MRI Human Brain Atlas (removed area around the brain)<br />
** Tutorial-Simple updated for Slicer 3.6.3 release<br />
** Tutorial-Advanced updated for Slicer 3.6.3 release<br />
** Tutorial tested for 101 training page<br />
** further work on the skull striper<br />
** work on integrating I/O function into base<br />
** Maintenance work for the Slicer 3.6.3 release<br />
** Atlas Creator Updates:<br />
*** fixed a huge bug which modified the orientation of images during save/load cycle<br />
*** added feature to create a unique output directory automatically<br />
*** added guess background level functionality using EMSegment logic for CMTK and BRAINSFit<br />
*** released AtlasCreator version 0.21 as a fully usable module<br />
*** created test and example section for created atlases ( http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Tests )<br />
**** including fixed and dynamic registrations using CMTK and BRAINSFit on 50 cases<br />
*** planned coming releases v0.3 and v0.4 http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator#Priority_List<br />
*** installed Slicer Trunk on SPL cluster<br />
**** commited required fixes to Slicer base<br />
**** documented on SPL Intweb ( https://intweb.spl.harvard.edu/Dell_Linux_Cluster#How_to_compile_3D_Slicer_3_on_the_cluster.3F )<br />
* 02/25/11<br />
** EMSegmenter Updates:<br />
*** CMTK: Added support for multiple scalartypes<br />
*** CMTK: set the backgroundLevel to get rid of the segmentation errors outside the target volume<br />
*** updated the MRI Human Brain atlas<br />
*** work on the skull striper<br />
*** use qsub for running Slicer tools in the cluster (batch mode)<br />
*** use xvfb for Slicer tools which use the X protocol<br />
** Atlas Creator Updates:<br />
*** introduced vtkMRMLAtlasCreatorNode<br />
**** It is possible to create a new AtlasCreator MRML Node and configure it<br />
**** the node can then be used to trigger an Atlas Creator computation by firing a Launch event<br />
*** introduced CMTK integration<br />
**** command line interface of the AtlasCreator supports adding the "--cmtk" flag to the command<br />
**** CMTK gets automatically detected, if installed as a Slicer extension<br />
*** optimized the handling of Double and Float images with BRAINSFit<br />
*** fixed and dynamic registration ran successfully on the SBIA cluster<br />
*** implemented the ability to listen to MRMLScene events in the Slicer3 Python Framework (Slicer Base)<br />
**** this enables listening to custom MRML Node events<br />
**** created small example on Slicer wiki: http://www.slicer.org/slicerWiki/index.php/Slicer3:Python:ProcessMRMLEvents<br />
*** provided mrml scene example for a fixed registration with 6 cases ( http://wiki.na-mic.org/Wiki/index.php/File:SceneFixed6Cases.zip )<br />
*** fixed bug in the Slicer3 Python Framework (Slicer Base) to exit Slicer correctly after using --evalpython<br />
*** created infrastructure to include C++ code in the AtlasCreator module using a GUI-less module approach<br />
**** included vtkImagePCAFilter and vtkImageKilianDistanceTransform as C++ filters successfully<br />
*** fixed overflow problem in connection with dynamic registration<br />
*** added the feature to remove all used temporary resources (cleanup)<br />
*** enabled the AtlasCreator C++ Code in the EMSegmentTclInterpreter (to test PCA filters)<br />
*** additional smaller fixes<br />
* 02/18/11<br />
** EMSegmenter Updates:<br />
*** Our Mac OS X Server is submitting 2 fresh nightly builds of the Slicer3/branch-3-6 and the Slicer3/trunk to the dashboard. The names are MORRICONE and MINKOWSKI.<br />
*** Slicer3 (with python support) has been successfully installed on UPenn's SBIA cluster. OS: CentOS release 5.5 (Final)<br />
*** Adjusted parameter for CMTK so that it can be used in a fast mode (below one hour) and in a accurate mode (multiple hours).<br />
*** EMSegmenter maintenance<br />
** Atlas Creator Updates:<br />
*** created a new command line interface (python atlascreator.py)<br />
**** including help and examples<br />
**** details available at the website http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator#The_Atlas_Creator_Command_Line_Interface<br />
*** fixed a blocker, where the resampled images where not used for Atlas generation<br />
*** found a BRAINSFit error in connection with dynamic registration which only appears on SPL machines<br />
**** investigated how to use CMTK as an alternative to BRAINSFit<br />
*** identified a problem with Slicer3 --evalpython<br />
*** commited a fix for a memory leak error when running the Atlas Creator<br />
*** Enabled code for PCA computation on local Slicer, still in the works, commited some fixes to specific SVN<br />
*** created and included UML diagrams on Wiki site<br />
*** created and included screenshots on Wiki site<br />
*** template now gets loaded into Slicer as well.<br />
*** temporary files are now saved in a subdirectory with a unique name so the Atlas Creator can be run multiple files without moving anything.<br />
*** in cluster mode, multi threading is now disabled.<br />
* 02/11/11<br />
** Installed MacOS and WindowsXP test machines<br />
** It is now possible to use a temporary directory with white spaces (this was a bug on Windows XP)<br />
** Added manual sampling to EMSegmenter module <br />
** Atlas Creator Updates:<br />
*** Generalized API to be able to run the Atlas Creator from external modules or using the Slicer launcher via command-line<br />
**** Used the opportunity to extensively comment the code<br />
*** Implemented Support for Parallelized Computation on a Cluster<br />
*** Finished Dynamic Registration against Mean of images<br />
*** Added mode to use existing transforms (f.e. to re-generate an Atlas)<br />
*** Added in-module help<br />
*** Smaller Fixes and Changes<br />
*** Merged latest version to Slicer 3.6.3 branch - ready for release<br />
*** Updated [[Projects:ARRA:SlicerEM:AtlasCreator]]<br />
* 02/04/11<br />
** option intermediate results directory is created for the user<br />
** clarified the usage, helped collaborators with the EMSegmenter<br />
** Windows specific runtime bug fixed, happened whenever we used an iterator two times.<br />
** Included detailed verbose printout in EMSegmentCommandLine<br />
** Added test results to MIDAS server<br />
** Use CMake to compare segmentation results with precomputed segmentation results<br />
** Further cleanup code (Number of registration flags simplified)<br />
** Simplified MRML structure(removed nodes)<br />
** Check if atlas files are properly downloaded to avoid FetchMI checksum checks<br />
** Fixed bug in test EMSegCL_IntermediateResults: "UpdateScene: error getting 0th storage node"<br />
** Updated template creator to new MRML structure ([[Projects:ARRA:SlicerEM#MRML_Structure|new MRML structure]])<br />
** Fixed the updated functionality for EMSegmenter<br />
*** also transferred fix to Extension wizard (was very quick)<br />
*** added new repository for 3.6.3 for EMSegment tasks<br />
*** fix for the new webserver index files and therefore do not need the index.html<br />
*** committed all code to 3.6.3 Branch and Trunk<br />
*** tested on Mac and Linux<br />
** Atlas Creator Updates:<br />
*** Created diagram of Atlas Creator workflow <br />
*** Support for Normalization of output Atlases done<br />
*** Support for Selecting the Output Cast done<br />
*** Re-Designed API<br />
**** Focus on Cluster proposal<br />
**** Focus on external invocation (command line or 3rd party module in 3D Slicer)<br />
*** Introduced Configuration Concept<br />
*** Documentation, Diagram and Priority List updated at [[Projects:ARRA:SlicerEM:AtlasCreator]]<br />
* 01/28/11<br />
** Fixed a bug in the test 'intermediateResultsDirectory'. The test doesn't use the results file which is specified in the mrml scene. Instead it is using a test specific results file(specified in the CMake template).<br />
** Fixed a Slicer4 bug : "ENH: Call the GeneralGauss(...) functions instead of the FastGauss(...) functions - this avoids type punning" Modules/EMSegment/Graph/vtkImageCurveRegion.cxx [15896]<br />
** Fixed a Slicer4 bug : "BUG: Use a normal gauss function to avoid type-punning" QTModules/EMSegment/Widgets/vtkPlotGaussian.cxx<br />
** Worked on the CT-Hand-Bone task<br />
** Worked on a EMSegmenter specific skull stripper<br />
** Atlas Creator Updates:<br />
*** Research and Proposal of running the Atlas Creator in a cluster environment<br />
*** Several GUI Fixes<br />
*** Support Dynamic Registration (in the works)<br />
*** Support for using existing Registrations by loading deformation fields (in the works)<br />
*** Support for Normalization of output Atlases (in the works)<br />
*** Support for Selecting the Output Cast (in the works)<br />
*** Merged Export of Deformation Fields and Export of Transforms<br />
* 01/21/11<br />
** Worked on new CT-Hand-Bone task<br />
** Maintaining work on existing tasks<br />
** Added new features to the Atlas Creator<br />
*** New wiki page [[Projects:ARRA:SlicerEM:AtlasCreator]]<br />
* 01/14/11<br />
** Created a test for the MRI-Human-Brain-Full-Parcellation task<br />
** Worked on failing tests if compiling Slicer3 with Superbuild<br />
** Worked on new CT-Hand-Bone task<br />
** Worked with Wendy on new ideas how to make FetchMI more rubust<br />
* 01/07/11<br />
** Created new Atlas Creator module for Slicer3<br />
** Created new Wiki page for [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-UseCaseAdvertisement Call for Datasets for the EM Segmenter Use Case Library]<br />
* 12/31/10<br />
** Help debugging FetchMI bugs [http://www.na-mic.org/Bug/view.php?id=1027 1027] [http://www.na-mic.org/Bug/view.php?id=983 983]<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain-Parcellation MRI-Human-Brain-Parcellation]<br />
* 12/24/10<br />
** Add postprocessing to segmentation, which includes island removal and subparcellation of tissue classes <br />
* 12/17/10<br />
** Added down-sampled image data for testing purposes<br />
** Added two tests for each task<br />
** Added UPenn logo to the EMSegmenter acknowledgment section<br />
** Work on FetchMI bugs<br />
** Updated Wiki page for the task MRI-Human-Brain-Parcellation<br />
* 12/10/10<br />
** Added wrapper for SkullStripperCLI to GenericTask.tcl<br />
** Updated CMTK extension, using now Torsten Rohlfing's repository: https://nitrc.org/svn/cmtk/tags/Slicer3<br />
** Updated Advanced Tutorial based on Ron's comments<br />
** Added functionality to threshold target image(s), negative values will be set to 0 so that the EMSegmenter can be used on those images<br />
* 12/03/10<br />
** Create a new Wiki page for the EMSegmenter Task Library [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks]<br />
** Updated task files and documentation<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain MRI-Human-Brain]<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain-Parcellation MRI-Human-Brain-Parcellation]<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:Non-Human-Primate Non-Human-Primate]<br />
** Fixed a apache server issue to update tasks in Slicer 3.6.2 <br />
* 11/26/10<br />
** Fixed bug: when creating new task that registration was performed regardless if it was selected or not<br />
** Worked on test cases for 'Non Human Primate' pipeline<br />
* 11/19/10<br />
** Created a new EMSegmenter Tutorial (simple mode) - (for quick results, no need to change parameters, this will be useful to clinicians)<br />
** Created a new EMSegmenter Tutorial (advanced mode) - for experienced user of the EMSegmenter<br />
** Created the new 'MRI Human Brain Parcellation' pipeline and added to 3D Slicer 3.6.2 (collaborators: Padmapriya Srinivasan and Sylvain Bouix, PNL BWH)<br />
* 11/12/10<br />
** Restructuring EMSegmenter's Tasks folder to support multiple pipelines<br />
** Start working on a 'MRI Human Brain Parcellation' pipeline (collaborators: Padmapriya Srinivasan and Sylvain Bouix, PNL BWH)<br />
** Start working on a 'Non Human Primate' pipeline (collaborators: Andriy Fedorov, BWH)<br />
** Slicer 3.6.2-RC2 maintenance<br />
* 11/05/10<br />
** software testing for Slicer 3.6.2 release<br />
** Added new test for option --intermediateResultsDirectory<br />
** Fixed bug 1023: MRML import doesn't read copied mrml scenes reliable<br />
** Fixed bug 1025: Slicer crashes when BRAINSFit returns error<br />
* 10/29/10<br />
** Pop up error message when performing segmentation<br />
** Add CMTK in Generic.tcl <br />
** BUG: use .mat extension for transformation files" GenericTask.tcl<br />
** Bug fixing with Slicer Base Code developers<br />
* 10/23/10<br />
** Bug fixes for Slicer 3.6.2 release<br />
** Memory leak fixed<br />
** comment-out unused code in MRI-Human-Brain.tcl<br />
* 10/15/10<br />
** Added function for automatically generating Template File <br />
** Added function for downloading task files from web<br />
** Added CMTK to extension module<br />
** One can assign now tcl file when creating a new task<br />
** Added class name to all tabs<br />
** Tested command line<br />
** Created virtual machines to submit tests reports to the dashboard<br />
** Created Popup window when an error message appears in pre-processing and segmentation<br />
** EMSegmenter works now with different image data types (short, float,...)<br />
** Removed several bugs in mrml structure<br />
<br />
* 10/8/10<br />
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory<br />
** Fixed the leaks in the nightly tests<br />
* 10/1/10<br />
** Removed command line nodes from mrml scene after the command line is executed<br />
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine<br />
** Added label - in addition to the tree - to show the selected anatomical tree node<br />
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)<br />
** Working on parallel execution of multiple instances of the EMSegmentCommandLine<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery><br />
<br />
<br />
=MRML Structure=<br />
<br />
<gallery heights=300px widths=600px perrow=2 caption="EM Segmenter - MRML Structure"><br />
Image:EMS MRML Structure 2010.png | EMS MRML Structure 2010<br />
Image:EMS MRML Structure 2011.png | EMS MRML Structure 2011<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=Annotation_Documentation&diff=66997Annotation Documentation2011-05-04T18:16:45Z<p>Pohl: </p>
<hr />
<div>[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM Return to ARRA Page]<br />
<br />
<br />
__NOTOC__<br />
===miAnnotation===<br />
miAnnotation (Medical Image Annotation)<br />
<br />
{|<br />
|[[Image:miAnnotation-GUI.jpg|thumb|560px|GUI]]<br />
|}<br />
<br />
== General Information ==<br />
This module is a work in progress targeted for release with [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 3D Slicer version 4]<br />
===Module Type & Category===<br />
<br />
Type: Interactive<br />
<br />
Category: Base <br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: pohl@csail.mit.edu<br />
* Daniel Haehn: haehn@bwh.harvard.edu<br />
* Past Contributors:<br />
** Yong Zhang: yzhang@bwh.harvard.edu<br />
<br />
===Module Description===<br />
The miAnnotation Module is designed for users to annotate medical images to capture information latent in the scans.<br />
<br />
== Usage ==<br />
Eight (8) different types of annotations can be created in the following ways: <br />
<br />
*Region Of Interest (ROI): Click on the ROI Icon [[File:miAnnotation-ROI.jpg]] on the middle panel of the miAnnotation main panel, a new ROI annotation will then be created on the right-hand-side 3D view. There are seven (7) control points on the ROI annotation for the user to interact with. The six (6) control points located on the six surface of the ROI box can be dragged using mouse left-button to enlarge or shrink the box. The one (1) control point located in the center of the box can be dragged using mouse left-button to relocate the box in the 3D view. A new ROI entry will also be created in the annotation table. The properties of the ROI annotation can be edited by clicking the edit icon [[File:miAnnotation-EditROI.jpg]] in the annotation table.<br />
<br />
*Text: Click on the text Icon [[File:miAnnotation-text.jpg]] on the middle panel of the miAnnotation main panel, a new text annotation will then be created on the right-hand-side 3D view. The default location of the new text annotation is on the bottom left corner of the viewer. The user can move the text annotation to any other locations by clicking and dragging the text annotation using the mouse middle-button. A new text entry will also be created in the annotation table. The content of the text annotation can be edited from the entry in the annotation table. The properties of the text annotation can be edited by clicking the edit icon [[File:miAnnotation-EditText.jpg]] in the annotation table.<br />
<br />
*Ruler: Click on the ruler Icon [[File:miAnnotation-ruler.jpg]] on the middle panel of the miAnnotation main panel, a new ruler annotation will then be created on the right-hand-side 3D view. The default location of the new ruler annotation is in the middle of the viewer spanned from left to right. The user can click and drag any one of the two control points of the ruler annotation to interact with it. A new ruler entry will also be created in the annotation table. The value of the ruler measurement can be automatically updated when the user interact with the ruler. The properties of the ruler annotation can be edited by clicking the edit icon [[File:miAnnotation-EditRuler.jpg]] in the annotation table.<br />
<br />
*Angle: Click on the angle Icon [[File:miAnnotation-angle.jpg]] on the middle panel of the miAnnotation main panel, a new angle annotation will then be initialized on the right-hand-side 3D view. The users are required to manually click three (3) times in the 3D viewer using mouse left-button to create the real angle annotation. After creating the angle annotation, the user can click and drag any one of the three control points of the angle annotation to interact with it. A new angle entry will also be created in the annotation table. The value of the angle measurement can be automatically updated when the user interact with the angle. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditAngle.jpg]] in the annotation table.<br />
<br />
*Fiducial: Click on the fiducial Icon [[File:miAnnotation-point.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in any of the 2D viewers using mouse left-button to create a new fiducial annotation. The new annotation will also be displayed in the 3D viewer. After creating the annotation, the user can click and drag it to interact with it. A new fiducial entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPoint.jpg]] in the annotation table.<br />
<br />
*Bidimensional Lines: Click on the bidimensional lines Icon [[File:miAnnotation-Polyline.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in the 3D viewers using mouse left-button to create two lines. These two lines are automatically orthogonal. After creating the annotation, the user can click and drag any of the four control points to interact with it. A new bidimensional line entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPolyline.jpg]] in the annotation table.<br />
<br />
*Spline: Click on the spline Icon [[File:miAnnotation-Spline.jpg]] on the middle panel of the miAnnotation main panel, then a new spline annotation point is created right in the center of the 3d viewer. The users are able to manually click and drag the spline point using mouse left-button to other locations in the 3D viewer. Up to five (5) points can be clicked and dragged from the initial location of the spline annotation. After creating the annotation, the user can click and drag any of the five control points to form different splines to fit their needs. Or the user can click and drag the entire spline annotation to move it as a whole. A new spline entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditSpline.jpg]] in the annotation table.<br />
<br />
*Sticky Note: Click on the stick note Icon [[File:miAnnotation-Note.jpg]] on the middle panel of the miAnnotation main panel, then a new stick note is created. There are no displays of the note in any of the 2D or 3D viewers. After creating the annotation, a new sticky note entry will be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditNote.jpg]] in the annotation table.<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for these use cases:<br />
<br />
* Use Case 1: This module is useful for basic measurements of volume, area, length, angle.<br />
* Use Case 2: Use eight different annotations to annotate medical images.<br />
<br />
===Tutorials===<br />
<br />
Links to tutorials explaining how to use this module:<br />
<br />
* Tutorial (coming soon)<br />
* Data Set (coming soon)<br />
<br />
===Quick Tour of Features and Use===<br />
* '''miAnnotation Main Panel''':<br />
{|<br />
|<br />
* '''Upper Panel:'''<br />
**8 different annotation types<br />
**controls for mouse modes<br />
<br />
<br />
<br />
<br />
<br />
<br />
* '''Middle Panel:'''<br />
**A table contains all annotations<br />
**Edit annotation properties<br />
**Edit annotation table<br />
<br />
<br />
<br />
<br />
<br />
* '''Lower Panel:'''<br />
**Save as text format<br />
**Save screen shot<br />
**Save entire MRML structure<br />
**Save report as HTML format<br />
<br />
|[[Image:miAnnotation-MainPanel.jpg|thumb|560px|Main Panel]]<br />
|}<br />
<br />
* '''Edit annotation table''':<br />
** Click hide/unhide icon [[File:miAnnotation-Visibility.jpg]] to hide and unhide a single annotation in the viewers<br />
** Click lock/unlock icon [[File:miAnnotation-Lock.jpg]] to lock and unlock a single annotation in the viewers to enable and disable the user interaction<br />
<br />
* '''Save Annotations''':<br />
{|<br />
|<br />
*Save screen shot<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
*Save entire MRML structure<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
*Save HTML<br />
|[[Image:miAnnotation-Screenshot.jpg|thumb|280px|Save Screen Shot]]<br />
[[Image:miAnnotation-MRML.jpg|thumb|280px|Save MRML Structure]]<br />
[[Image:miAnnotation-HTML.jpg|thumb|280px|Save HTML Format]]<br />
|}<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
miAnnotation is not part of Slicer3.6. To use the module, you have to use the trunk version of the Slicer3. See [http://www.slicer.org/slicerWiki/index.php/Slicer4:Build_Instructions the build instructions].<br />
<br />
===Dependencies===<br />
<br />
Fiducials and Measurements Modules are currently needed. Later these will be integrated into a unified Annotations module.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* vtkSlicermiAnnotationModuleLogicTest1.cxx<br />
* vtkMRMLAnnotationStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationRulerStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationRulerNodeTest1.cxx<br />
* vtkMRMLAnnotationPointDisplayNodeTest1.cxx<br />
* vtkMRMLAnnotationNodeTest1.cxx<br />
* vtkMRMLAnnotationLinesStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationLinesNodeTest1.cxx<br />
* vtkMRMLAnnotationLineDisplayNodeTest1.cxx<br />
* vtkMRMLAnnotationFiducialsStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationFiducialNodeTest1.cxx<br />
* vtkMRMLAnnotationDisplayNodeTest1.cxx<br />
* vtkMRMLAnnotationControlPointsStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationControlPointsNodeTest1.cxx<br />
* vtkMRMLAnnotationAngleStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationAngleNodeTest1.cxx<br />
* qSlicermiAnnotationModuleAnnotationPropertyDialogTest1.cxx<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Source Code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/QTModules/miAnnotation/<br />
<br />
UML class diagrams of selected functionalities:<br />
[[Image:Annotation Module TextNodes Class Diagram.png|thumb|left|Classes involved in adding Text annotations]]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is supported by an [[Projects:ARRA:SlicerAM | ARRA supplement to the Neuroimage Analysis Center (NAC), an NCRR Resource Center, NIH NCRR grant P41 RR13218]]. <br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005419.<br />
<br />
===References===<br />
<br />
<!--<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
--></div>Pohlhttps://www.na-mic.org/w/index.php?title=Annotation_Documentation&diff=66995Annotation Documentation2011-05-04T18:15:57Z<p>Pohl: moved MiAnnotation Documentation to Annotation Documentation</p>
<hr />
<div>[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM Return to miAnnotation]<br />
<br />
<br />
__NOTOC__<br />
===miAnnotation===<br />
miAnnotation (Medical Image Annotation)<br />
<br />
{|<br />
|[[Image:miAnnotation-GUI.jpg|thumb|560px|GUI]]<br />
|}<br />
<br />
== General Information ==<br />
This module is a work in progress targeted for release with [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 3D Slicer version 4]<br />
===Module Type & Category===<br />
<br />
Type: Interactive<br />
<br />
Category: Base <br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: pohl@csail.mit.edu<br />
* Daniel Haehn: haehn@bwh.harvard.edu<br />
* Past Contributors:<br />
** Yong Zhang: yzhang@bwh.harvard.edu<br />
<br />
===Module Description===<br />
The miAnnotation Module is designed for users to annotate medical images to capture information latent in the scans.<br />
<br />
== Usage ==<br />
Eight (8) different types of annotations can be created in the following ways: <br />
<br />
*Region Of Interest (ROI): Click on the ROI Icon [[File:miAnnotation-ROI.jpg]] on the middle panel of the miAnnotation main panel, a new ROI annotation will then be created on the right-hand-side 3D view. There are seven (7) control points on the ROI annotation for the user to interact with. The six (6) control points located on the six surface of the ROI box can be dragged using mouse left-button to enlarge or shrink the box. The one (1) control point located in the center of the box can be dragged using mouse left-button to relocate the box in the 3D view. A new ROI entry will also be created in the annotation table. The properties of the ROI annotation can be edited by clicking the edit icon [[File:miAnnotation-EditROI.jpg]] in the annotation table.<br />
<br />
*Text: Click on the text Icon [[File:miAnnotation-text.jpg]] on the middle panel of the miAnnotation main panel, a new text annotation will then be created on the right-hand-side 3D view. The default location of the new text annotation is on the bottom left corner of the viewer. The user can move the text annotation to any other locations by clicking and dragging the text annotation using the mouse middle-button. A new text entry will also be created in the annotation table. The content of the text annotation can be edited from the entry in the annotation table. The properties of the text annotation can be edited by clicking the edit icon [[File:miAnnotation-EditText.jpg]] in the annotation table.<br />
<br />
*Ruler: Click on the ruler Icon [[File:miAnnotation-ruler.jpg]] on the middle panel of the miAnnotation main panel, a new ruler annotation will then be created on the right-hand-side 3D view. The default location of the new ruler annotation is in the middle of the viewer spanned from left to right. The user can click and drag any one of the two control points of the ruler annotation to interact with it. A new ruler entry will also be created in the annotation table. The value of the ruler measurement can be automatically updated when the user interact with the ruler. The properties of the ruler annotation can be edited by clicking the edit icon [[File:miAnnotation-EditRuler.jpg]] in the annotation table.<br />
<br />
*Angle: Click on the angle Icon [[File:miAnnotation-angle.jpg]] on the middle panel of the miAnnotation main panel, a new angle annotation will then be initialized on the right-hand-side 3D view. The users are required to manually click three (3) times in the 3D viewer using mouse left-button to create the real angle annotation. After creating the angle annotation, the user can click and drag any one of the three control points of the angle annotation to interact with it. A new angle entry will also be created in the annotation table. The value of the angle measurement can be automatically updated when the user interact with the angle. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditAngle.jpg]] in the annotation table.<br />
<br />
*Fiducial: Click on the fiducial Icon [[File:miAnnotation-point.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in any of the 2D viewers using mouse left-button to create a new fiducial annotation. The new annotation will also be displayed in the 3D viewer. After creating the annotation, the user can click and drag it to interact with it. A new fiducial entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPoint.jpg]] in the annotation table.<br />
<br />
*Bidimensional Lines: Click on the bidimensional lines Icon [[File:miAnnotation-Polyline.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in the 3D viewers using mouse left-button to create two lines. These two lines are automatically orthogonal. After creating the annotation, the user can click and drag any of the four control points to interact with it. A new bidimensional line entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPolyline.jpg]] in the annotation table.<br />
<br />
*Spline: Click on the spline Icon [[File:miAnnotation-Spline.jpg]] on the middle panel of the miAnnotation main panel, then a new spline annotation point is created right in the center of the 3d viewer. The users are able to manually click and drag the spline point using mouse left-button to other locations in the 3D viewer. Up to five (5) points can be clicked and dragged from the initial location of the spline annotation. After creating the annotation, the user can click and drag any of the five control points to form different splines to fit their needs. Or the user can click and drag the entire spline annotation to move it as a whole. A new spline entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditSpline.jpg]] in the annotation table.<br />
<br />
*Sticky Note: Click on the stick note Icon [[File:miAnnotation-Note.jpg]] on the middle panel of the miAnnotation main panel, then a new stick note is created. There are no displays of the note in any of the 2D or 3D viewers. After creating the annotation, a new sticky note entry will be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditNote.jpg]] in the annotation table.<br />
<br />
===Use Cases, Examples===<br />
<br />
This module is especially appropriate for these use cases:<br />
<br />
* Use Case 1: This module is useful for basic measurements of volume, area, length, angle.<br />
* Use Case 2: Use eight different annotations to annotate medical images.<br />
<br />
===Tutorials===<br />
<br />
Links to tutorials explaining how to use this module:<br />
<br />
* Tutorial (coming soon)<br />
* Data Set (coming soon)<br />
<br />
===Quick Tour of Features and Use===<br />
* '''miAnnotation Main Panel''':<br />
{|<br />
|<br />
* '''Upper Panel:'''<br />
**8 different annotation types<br />
**controls for mouse modes<br />
<br />
<br />
<br />
<br />
<br />
<br />
* '''Middle Panel:'''<br />
**A table contains all annotations<br />
**Edit annotation properties<br />
**Edit annotation table<br />
<br />
<br />
<br />
<br />
<br />
* '''Lower Panel:'''<br />
**Save as text format<br />
**Save screen shot<br />
**Save entire MRML structure<br />
**Save report as HTML format<br />
<br />
|[[Image:miAnnotation-MainPanel.jpg|thumb|560px|Main Panel]]<br />
|}<br />
<br />
* '''Edit annotation table''':<br />
** Click hide/unhide icon [[File:miAnnotation-Visibility.jpg]] to hide and unhide a single annotation in the viewers<br />
** Click lock/unlock icon [[File:miAnnotation-Lock.jpg]] to lock and unlock a single annotation in the viewers to enable and disable the user interaction<br />
<br />
* '''Save Annotations''':<br />
{|<br />
|<br />
*Save screen shot<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
*Save entire MRML structure<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
*Save HTML<br />
|[[Image:miAnnotation-Screenshot.jpg|thumb|280px|Save Screen Shot]]<br />
[[Image:miAnnotation-MRML.jpg|thumb|280px|Save MRML Structure]]<br />
[[Image:miAnnotation-HTML.jpg|thumb|280px|Save HTML Format]]<br />
|}<br />
<br />
== Development ==<br />
<br />
===Notes from the Developer(s)===<br />
<br />
miAnnotation is not part of Slicer3.6. To use the module, you have to use the trunk version of the Slicer3. See [http://www.slicer.org/slicerWiki/index.php/Slicer4:Build_Instructions the build instructions].<br />
<br />
===Dependencies===<br />
<br />
Fiducials and Measurements Modules are currently needed. Later these will be integrated into a unified Annotations module.<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* vtkSlicermiAnnotationModuleLogicTest1.cxx<br />
* vtkMRMLAnnotationStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationRulerStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationRulerNodeTest1.cxx<br />
* vtkMRMLAnnotationPointDisplayNodeTest1.cxx<br />
* vtkMRMLAnnotationNodeTest1.cxx<br />
* vtkMRMLAnnotationLinesStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationLinesNodeTest1.cxx<br />
* vtkMRMLAnnotationLineDisplayNodeTest1.cxx<br />
* vtkMRMLAnnotationFiducialsStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationFiducialNodeTest1.cxx<br />
* vtkMRMLAnnotationDisplayNodeTest1.cxx<br />
* vtkMRMLAnnotationControlPointsStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationControlPointsNodeTest1.cxx<br />
* vtkMRMLAnnotationAngleStorageNodeTest1.cxx<br />
* vtkMRMLAnnotationAngleNodeTest1.cxx<br />
* qSlicermiAnnotationModuleAnnotationPropertyDialogTest1.cxx<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
Source Code:<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/QTModules/miAnnotation/<br />
<br />
UML class diagrams of selected functionalities:<br />
[[Image:Annotation Module TextNodes Class Diagram.png|thumb|left|Classes involved in adding Text annotations]]<br />
<br />
== More Information == <br />
<br />
===Acknowledgment===<br />
This work is supported by an [[Projects:ARRA:SlicerAM | ARRA supplement to the Neuroimage Analysis Center (NAC), an NCRR Resource Center, NIH NCRR grant P41 RR13218]]. <br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005419.<br />
<br />
===References===<br />
<br />
<!--<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
--></div>Pohlhttps://www.na-mic.org/w/index.php?title=MiAnnotation_Documentation&diff=66996MiAnnotation Documentation2011-05-04T18:15:57Z<p>Pohl: moved MiAnnotation Documentation to Annotation Documentation</p>
<hr />
<div>#REDIRECT [[Annotation Documentation]]</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM:AtlasCreator&diff=64693Projects:ARRA:SlicerEM:AtlasCreator2011-02-26T03:48:49Z<p>Pohl: /* Priority List */</p>
<hr />
<div>= Atlas Creator =<br />
<br />
The Atlas Creator combines existing segmentations to an anatomical atlas based on robust statistics.<br />
<br />
== Examples ==<br />
<br />
Examples have to be re-generated.. Coming soon!<br />
<br />
== GUI ==<br />
<br />
The following screenshot shows the graphical user interface of the Atlas Creator module in 3D Slicer Version 3.<br />
<br />
[[File:Atlascreator.png]]<br />
<br />
== Priority List ==<br />
<br />
The priority list reflects the open issues.<br />
<br />
# <strike>Re-structure Atlas Creator code according to the Design specified below</strike><br />
# <strike>Implement dynamic registration</strike><br />
#* <strike>Watch out for overflows</strike><br />
# <strike>Implement support for parallel Computation</strike><br />
# <strike>Add Help</strike> and Online Documentation<br />
# <strike>check how to include C++ code in AtlasCreator</strike><br />
#* <strike>create concept</strike><br />
# <strike>make KilisSandbox work with PCA</strike><br />
# create AtlasCreator MRML Node (80%)<br />
# update documentation page<br />
# include CMTK as alternative to BRAINSFit (99%)<br />
# Include PCA functionality in AtlasCreator<br />
# add the ability to normalize to 0..X instead of only 0..1<br />
# create outputDir automatically<br />
# add ability to specify wait time for cluster mode<br />
# <strike>Solve Double/Float Problem</strike><br />
# also return as output the normalized intensity maps of aligned cases in the static mode<br />
<br />
== Design ==<br />
<br />
The following State Machine diagram shows the flow of the Atlas Creator logic. It can be run in two modes:<br />
* Normal mode, all computations on one machine<br />
* Cluster mode, parallelized computations<br />
<br />
[[File:AtlasCreatorStateMachine.png|600px]]<br />
<br />
<br />
The following class diagram shows the structure of the module.<br />
<br />
[[File:AtlasCreatorClassDiagramm.png|600px]]<br />
<br />
=== Proposal: Configuration of the Atlas Creator logic ===<br />
<br />
The Atlas Creator supports different modes of operation. For now, we focus on Skip Registration Mode, Normal Mode and Cluster Mode.<br />
<br />
To configure an Atlas Creator operation, we introduce configuration containers. The following example shows how to create the configuration:<br />
<pre><br />
# configuration for a Normal Mode operation<br />
configuration = AtlasCreatorConfiguration()<br />
# define the parameters<br />
configuration.SetTemplateType("fixed")<br />
...<br />
self._logic.Start(configuration)<br />
<br />
# configuration for a Cluster Mode operation<br />
gridConfiguration = AtlasCreatorGridConfiguration()<br />
# define the same parameters as above<br />
gridConfiguration.SetTemplateType("fixed")<br />
...<br />
# and also additional cluster specific parameters<br />
gridConfiguration.SetSchedulerCommand("stageClusterJob.sh")<br />
...<br />
self._logic.Start(configuration)<br />
</pre><br />
<br />
The logic detects which operation scenario was configured and then adjusts the workflow accordingly. This concept can be easily extended for future operation modes.<br />
<br />
=== Proposal: Running the Atlas Creator in a Grid Environment ===<br />
<br />
The Atlas Creator concept supports parallelized computations. An existing grid environment can be leveraged during the Registration phase as shown in the diagram above.<br />
<br />
Only the Registration can be performed parallelized since it is the most time-consuming task in the Atlas Creator pipeline.<br />
<br />
The Atlas Creator module runs on one node in the cluster (most likely the head node) and then generates bash scripts which start the registration using the 3D Slicer launch mechanism. These scripts can be run using an existing scheduler or a similar mechanism and use the Python invokation method shown in the section below. An existing $DISPLAY environment is not necessary for using the 3D Slicer launch mechanism.<br />
<br />
The module immediately recognizes if the parallelized registration jobs are complete and then continues the pipeline on the node where the it was first started.<br />
<br />
=== The Atlas Creator Command Line Interface ===<br />
<br />
The Atlas Creator comes with a command line interface. This interface can be used by invoking the following command.<br />
<br />
<pre><br />
# in the source directory<br />
cd Slicer3/Modules/AtlasCreator/<br />
<br />
# or in the build directory<br />
cd Slicer3-build/lib/Slicer3/Modules/AtlasCreator/<br />
<br />
# start the command line interface<br />
python atlascreator.py<br />
</pre><br />
<br />
A detailed help system is available by calling '''python atlascreator.py --help''':<br />
<pre><br />
21:42:17 daniel@sbia-pc66:~/SLICER/TRUNK/Slicer3/Modules/AtlasCreator$ python atlascreator.py --help<br />
AtlasCreator for 3D Slicer<br />
Version v0.1<br />
<br />
Usage:<br />
<br />
-h, --help<br />
Show this information.<br />
<br />
-i, --images DIR<br />
Directory containing original images.<br />
<br />
-s, --segmentations DIR<br />
Directory containing segmentations.<br />
<br />
-o, --output DIR<br />
Output directory.<br />
<br />
--skipRegistration<br />
Skip the registration and use existing transforms.<br />
<br />
The following arguments have to be specified if the registration is skipped:<br />
<br />
--transforms DIR<br />
Directory containing existing transforms.<br />
<br />
--existingTemplate FILEPATH<br />
Filepath to an existing template used for resampling only.<br />
<br />
--dynamic<br />
Use a dynamic template for registration based on means of images.<br />
<br />
The following arguments have to be specified if dynamic registration is chosen:<br />
<br />
-m, --meanIterations INT<br />
Number of iterations to compute and register against a mean image.<br />
<br />
--fixed<br />
Use a fixed template for registration.<br />
<br />
The following arguments have to be specified if fixed registration is chosen:<br />
<br />
--template FILEPATH<br />
Filepath to an image used as a template for fixed registration.<br />
<br />
-n, --non-rigid<br />
Use Non-Rigid registration additionally.<br />
<br />
-w, --writeTransforms<br />
Write transforms to output directory.<br />
<br />
-l, --labels STRING<br />
List of labels to include for the atlases, f.e. "3 4 5 6 8 10".<br />
<br />
--normalize<br />
Normalize Atlases to 0..1.<br />
If activated, the output cast will be set to Float.<br />
<br />
--outputCast INT<br />
Output cast for the atlases. Possible values:<br />
0: Char<br />
1: Unsigned Char<br />
2: Double<br />
3: Float<br />
4: Int<br />
5: Unsigned Int<br />
6: Long<br />
7: Unsigned Long<br />
8: Short<br />
9: Unsigned Short<br />
DEFAULT: 8<br />
<br />
-c, --cluster<br />
Use the cluster mode.<br />
<br />
The following arguments have to be specified if cluster mode is chosen:<br />
<br />
--schedulerCommand EXECUTABLE<br />
The executable to use as a scheduler in cluster mode, f.e. "qsub-run".<br />
<br />
--slicer FILEPATH<br />
Filepath to the 3D Slicer launcher including arguments, f.e. "/usr/bin/Slicer3 --tmp_dir /var/tmp".<br />
DEFAULT: Find the 3D Slicer launcher automatically.<br />
<br />
-d, --debug<br />
Enable debug information.<br />
<br />
--dryrun<br />
Output executable commands instead of running the registration or resampling.<br />
<br />
--examples<br />
Show usage examples.<br />
<br />
<br />
Developed by Daniel Haehn and Kilian Pohl, University of Pennsylvania. The research was funded by an ARRA supplement to NIH NCRR (P41 RR13218).<br />
<br />
Thanks to everyone!<br />
<br />
</pre><br />
<br />
Usage examples can be displayed by calling '''python atlascreator.py --examples''':<br />
<pre><br />
21:42:13 daniel@sbia-pc66:~/SLICER/TRUNK/Slicer3/Modules/AtlasCreator$ python atlascreator.py --examples<br />
AtlasCreator for 3D Slicer<br />
Version v0.1<br />
<br />
Examples:<br />
-----------------------------------------------------------------------------------------------<br />
1. Run fixed registration with the testdata:<br />
<br />
python atlascreator.py -i TestData/originals/ -s TestData/segmentations/ -o /tmp/acout --fixed --template TestData/originals/case62.nrrd -w -l "3 4 5 6 7 8 9" --normalize<br />
<br />
-----------------------------------------------------------------------------------------------<br />
2. Run dynamic registration with the testdata:<br />
<br />
python atlascreator.py -i TestData/originals/ -s TestData/segmentations/ -o /tmp/acout --dynamic --meanIterations 5 -w -l "3 4 5 6 7 8 9" --normalize<br />
<br />
-----------------------------------------------------------------------------------------------<br />
3. Run dynamic registration with the testdata on a cluster (scheduler command "qsub-run"):<br />
<br />
python atlascreator.py -i TestData/originals/ -s TestData/segmentations/ -o /tmp/acout --dynamic --meanIterations 5 -w -l "3 4 5 6 7 8 9" --normalize --cluster --schedulerCommand qsub-run<br />
<br />
-----------------------------------------------------------------------------------------------<br />
4. Use existing registrations and just re-sample<br />
<br />
python atlascreator.py --skipRegistration --transforms /tmp/acout --existingTemplate TestData/segmentations/case62.nrrd -s TestData/segmentations/ -o /tmp/acout -l "3 4 5 6 7 8 9" --normalize --outputCast 3<br />
<br />
</pre><br />
<br />
==== Invoking the Atlas Creator logic externally ====<br />
The Atlas Creator logic can be invoked via Python, f.e. from another 3D Slicer module or the 3D Slicer Python console.<br />
<br />
To access the Atlas Creator logic, the following snippet is useful:<br />
<br />
<pre><br />
from Slicer import slicer<br />
<br />
# get the path to the Atlas Creator module<br />
pathToAtlasCreator = str(slicer.Application.GetModulePaths()) + '/AtlasCreator'<br />
<br />
# add it to the python sys path<br />
sys.path.append(pathToAtlasCreator)<br />
<br />
# import the Atlas Creator module<br />
from AtlasCreatorGUI import *<br />
<br />
# instantiate the Atlas Creator gui, needed for debug statements on the console<br />
# and automatically creates the logic<br />
gui = AtlasCreatorGUI()<br />
<br />
# get the Atlas Creator logic<br />
logic = gui.GetMyLogic()<br />
<br />
# create configuration<br />
configuration = AtlasCreatorConfiguration()<br />
# configure now using the setters...<br />
<br />
# work with the logic<br />
logic.Start(configuration)<br />
</pre></div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=64197Projects:ARRA:SlicerEM2011-02-07T05:02:21Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 07/02/11<br />
** Installed MacOS and WindowsXP test machines<br />
** It is now possible to use a temporary directory with white spaces (this was a bug on Windows XP)<br />
** Added manual sampling to EMSegmenter module <br />
* 04/02/11<br />
** option intermediate results directory is created for the user<br />
** clarified the usage, helped collaborators with the EMSegmenter<br />
** Windows specific runtime bug fixed, happened whenever we used an iterator two times.<br />
** Included detailed verbose printout in EMSegmentCommandLine<br />
** Added test results to MIDAS server<br />
** Use CMake to compare segmentation results with precomputed segmentation results<br />
** Further cleanup code (Number of registration flags simplified)<br />
** Simplified MRML structure(removed nodes)<br />
** Check if atlas files are properly downloaded to avoid FetchMI checksum checks<br />
** Fixed bug in test EMSegCL_IntermediateResults: "UpdateScene: error getting 0th storage node"<br />
** Updated template creator to new MRML structure ([[Projects:ARRA:SlicerEM#MRML_Structure|new MRML structure]])<br />
* 04/02/11<br />
** Fixed the updated functionality for EMSegmenter<br />
*** also transferred fix to Extension wizard (was very quick)<br />
*** added new repository for 3.6.3 for EMSegment tasks<br />
*** fix for the new webserver index files and therefore do not need the index.html<br />
*** committed all code to 3.6.3 Branch and Trunk<br />
*** tested on Mac and Linux<br />
** Atlas Creator Updates:<br />
*** Created diagram of Atlas Creator workflow <br />
*** Support for Normalization of output Atlases done<br />
*** Support for Selecting the Output Cast done<br />
*** Re-Designed API<br />
**** Focus on Cluster proposal<br />
**** Focus on external invocation (command line or 3rd party module in 3D Slicer)<br />
*** Introduced Configuration Concept<br />
*** Documentation, Diagram and Priority List updated at [[Projects:ARRA:SlicerEM:AtlasCreator]]<br />
* 28/01/11<br />
** Fixed a bug in the test 'intermediateResultsDirectory'. The test doesn't use the results file which is specified in the mrml scene. Instead it is using a test specific results file(specified in the CMake template).<br />
** Fixed a Slicer4 bug : "ENH: Call the GeneralGauss(...) functions instead of the FastGauss(...) functions - this avoids type punning" Modules/EMSegment/Graph/vtkImageCurveRegion.cxx [15896]<br />
** Fixed a Slicer4 bug : "BUG: Use a normal gauss function to avoid type-punning" QTModules/EMSegment/Widgets/vtkPlotGaussian.cxx<br />
** Worked on the CT-Hand-Bone task<br />
** Worked on a EMSegmenter specific skull stripper<br />
** Atlas Creator Updates:<br />
*** Research and Proposal of running the Atlas Creator in a cluster environment<br />
*** Several GUI Fixes<br />
*** Support Dynamic Registration (in the works)<br />
*** Support for using existing Registrations by loading deformation fields (in the works)<br />
*** Support for Normalization of output Atlases (in the works)<br />
*** Support for Selecting the Output Cast (in the works)<br />
*** Merged Export of Deformation Fields and Export of Transforms<br />
* 21/01/11<br />
** Worked on new CT-Hand-Bone task<br />
** Maintaining work on existing tasks<br />
** Added new features to the Atlas Creator<br />
*** New wiki page [[Projects:ARRA:SlicerEM:AtlasCreator]]<br />
* 14/01/11<br />
** Created a test for the MRI-Human-Brain-Full-Parcellation task<br />
** Worked on failing tests if compiling Slicer3 with Superbuild<br />
** Worked on new CT-Hand-Bone task<br />
** Worked with Wendy on new ideas how to make FetchMI more rubust<br />
* 07/01/11<br />
** Created new Atlas Creator module for Slicer3<br />
** Created new Wiki page for [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-UseCaseAdvertisement Call for Datasets for the EM Segmenter Use Case Library]<br />
* 12/31/10<br />
** Help debugging FetchMI bugs [http://www.na-mic.org/Bug/view.php?id=1027 1027] [http://www.na-mic.org/Bug/view.php?id=983 983]<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain-Parcellation MRI-Human-Brain-Parcellation]<br />
* 12/24/10<br />
** Add postprocessing to segmentation, which includes island removal and subparcellation of tissue classes <br />
* 12/17/10<br />
** Added down-sampled image data for testing purposes<br />
** Added two tests for each task<br />
** Added UPenn logo to the EMSegmenter acknowledgment section<br />
** Work on FetchMI bugs<br />
** Updated Wiki page for the task MRI-Human-Brain-Parcellation<br />
* 12/10/10<br />
** Added wrapper for SkullStripperCLI to GenericTask.tcl<br />
** Updated CMTK extension, using now Torsten Rohlfing's repository: https://nitrc.org/svn/cmtk/tags/Slicer3<br />
** Updated Advanced Tutorial based on Ron's comments<br />
** Added functionality to threshold target image(s), negative values will be set to 0 so that the EMSegmenter can be used on those images<br />
* 12/03/10<br />
** Create a new Wiki page for the EMSegmenter Task Library [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks]<br />
** Updated task files and documentation<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain MRI-Human-Brain]<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain-Parcellation MRI-Human-Brain-Parcellation]<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:Non-Human-Primate Non-Human-Primate]<br />
** Fixed a apache server issue to update tasks in Slicer 3.6.2 <br />
* 11/26/10<br />
** Fixed bug: when creating new task that registration was performed regardless if it was selected or not<br />
** Worked on test cases for 'Non Human Primate' pipeline<br />
* 11/19/10<br />
** Created a new EMSegmenter Tutorial (simple mode) - (for quick results, no need to change parameters, this will be useful to clinicians)<br />
** Created a new EMSegmenter Tutorial (advanced mode) - for experienced user of the EMSegmenter<br />
** Created the new 'MRI Human Brain Parcellation' pipeline and added to 3D Slicer 3.6.2 (collaborators: Padmapriya Srinivasan and Sylvain Bouix, PNL BWH)<br />
* 11/12/10<br />
** Restructuring EMSegmenter's Tasks folder to support multiple pipelines<br />
** Start working on a 'MRI Human Brain Parcellation' pipeline (collaborators: Padmapriya Srinivasan and Sylvain Bouix, PNL BWH)<br />
** Start working on a 'Non Human Primate' pipeline (collaborators: Andriy Fedorov, BWH)<br />
** Slicer 3.6.2-RC2 maintenance<br />
* 11/05/10<br />
** software testing for Slicer 3.6.2 release<br />
** Added new test for option --intermediateResultsDirectory<br />
** Fixed bug 1023: MRML import doesn't read copied mrml scenes reliable<br />
** Fixed bug 1025: Slicer crashes when BRAINSFit returns error<br />
* 10/29/10<br />
** Pop up error message when performing segmentation<br />
** Add CMTK in Generic.tcl <br />
** BUG: use .mat extension for transformation files" GenericTask.tcl<br />
** Bug fixing with Slicer Base Code developers<br />
* 10/23/10<br />
** Bug fixes for Slicer 3.6.2 release<br />
** Memory leak fixed<br />
** comment-out unused code in MRI-Human-Brain.tcl<br />
* 10/15/10<br />
** Added function for automatically generating Template File <br />
** Added function for downloading task files from web<br />
** Added CMTK to extension module<br />
** One can assign now tcl file when creating a new task<br />
** Added class name to all tabs<br />
** Tested command line<br />
** Created virtual machines to submit tests reports to the dashboard<br />
** Created Popup window when an error message appears in pre-processing and segmentation<br />
** EMSegmenter works now with different image data types (short, float,...)<br />
** Removed several bugs in mrml structure<br />
<br />
* 10/8/10<br />
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory<br />
** Fixed the leaks in the nightly tests<br />
* 10/1/10<br />
** Removed command line nodes from mrml scene after the command line is executed<br />
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine<br />
** Added label - in addition to the tree - to show the selected anatomical tree node<br />
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)<br />
** Working on parallel execution of multiple instances of the EMSegmentCommandLine<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery><br />
<br />
<br />
=MRML Structure=<br />
<br />
<gallery heights=300px widths=600px perrow=2 caption="EM Segmenter - MRML Structure"><br />
Image:EMS MRML Structure 2010.png | EMS MRML Structure 2010<br />
Image:EMS MRML Structure 2011.png | EMS MRML Structure 2011<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=Resources&diff=63970Resources2011-01-24T20:43:43Z<p>Pohl: /* Active Job Openings */</p>
<hr />
<div>=== [[Collaborator:Resources|Resources for Collaborators]] ===<br />
<br />
[[Collaborator:Resources|This page]] contains information for investigators who would like to collaborate with NAMIC.<br />
<br />
=== Software, Data, and Tutorials ===<br />
<br />
NA-MIC Software, Data, and Tutorials are available at the following link: [[Downloads|NA-MIC Downloads]].<br />
<br />
=== Software: NA-MIC kit ===<br />
<br />
The NA-MIC Kit consists of all software that is being made available under the NA-MIC project. This software follows the NIH guidelines for open software development. In this section, we provide information about the components of the NA-MIC kit as well as supporting software tools that are being used by the software developers on the project.<br />
<br />
* [[NA-MIC-Kit|Software Resources for NA-MIC Kit]]<br />
* [[Engineering:SandBox|Development Sandbox ]]<br />
<br />
=== Acknowledgment for NA-MIC Support ===<br />
<br />
To acknowledge NA-MIC in your publications or software, please use the text provided [[Publications:NIH_Roadmap_acknowledgement|here]].<br />
<br />
=== Mailing Lists ===<br />
<br />
These are the mailing lists associated with NA-MIC. If you are a participant in the project, please make sure that you are signed up for all the mailing lists that apply to your role and interests in the projects. These lists are moderated and maintained by Kitware.<br />
<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-leadership NAMIC Leadership] (All Core and Site PIs, Administrators)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-algo-pi NAMIC Algo PIs] (Algorithms Site PIs)<br />
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* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-service NAMIC-Service] (Service Core)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-training NAMIC Training] (Training Core)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-dissemination NAMIC-dissemination] (Dissemination Core)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-EAB NAMIC-EAB] (EAB)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-nih NAMIC-nih] (NIH programs staff)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-collaborators NAMIC-collaborators]<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-alumni NAMIC-Alumni] (Alumni)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-info NAMIC-info]<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week NAMIC Project Week]<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-all NAMIC All]<br />
<br />
=== [[NIH-Page|NIH Page]] ===<br />
<br />
* [[NIH-Page|This page]] contains useful information provided by our NIH officers.<br />
<br />
=== [[NAMIC_Logos_Templates|NAMIC Logos and Templates]] ===<br />
<br />
* [[NAMIC_Logos_Templates|This page]] contains links to files containing the NA-MIC logo and templates.<br />
<br />
=== Active Job Openings ===<br />
* [[2010.07.25-KitwareJob | Kitware Job: Open-Source Developers for Digital Libraries, Bioinformatics, and Information Visualization]]<br />
* [[Media:Intuitive_Surgical_Senior_Research_Engineer-Software-and-UI_2010-12-1a.pdf| Intuitive Surgical Job: Senior Research Engineer - Software and UI]]<br />
*[[Media:2011_January_CONDR_Postdoc_Description.pdf|WUSTL Postdoctoral Fellow]]. Posted January 24, 2011<br />
<br />
=== Wikis ===<br />
<br />
We are often asked about mediawiki and other wikis. Here is some [[Information_on_wikis|information on wikis]].</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=62703Projects:ARRA:SlicerEM2010-12-29T02:11:07Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 12/24/10<br />
** Add postprocessing to segmentation, which includes island removal and subparcellation of tissue classes <br />
* 12/17/10<br />
** Added down-sampled image data for testing purposes<br />
** Added two tests for each task<br />
** Added UPenn logo to the EMSegmenter acknowledgment section<br />
** Work on FetchMI bugs<br />
** Updated Wiki page for the task MRI-Human-Brain-Parcellation<br />
* 12/10/10<br />
** Added wrapper for SkullStripperCLI to GenericTask.tcl<br />
** Updated CMTK extension, using now Torsten Rohlfing's repository: https://nitrc.org/svn/cmtk/tags/Slicer3<br />
** Updated Advanced Tutorial based on Ron's comments<br />
** Added functionality to threshold target image(s), negative values will be set to 0 so that the EMSegmenter can be used on those images<br />
* 12/03/10<br />
** Create a new Wiki page for the EMSegmenter Task Library [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks]<br />
** Updated task files and documentation<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain MRI-Human-Brain]<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain-Parcellation MRI-Human-Brain-Parcellation]<br />
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:Non-Human-Primate Non-Human-Primate]<br />
** Fixed a apache server issue to update tasks in Slicer 3.6.2 <br />
* 11/26/10<br />
** Fixed bug: when creating new task that registration was performed regardless if it was selected or not<br />
** Worked on test cases for 'Non Human Primate' pipeline<br />
* 11/19/10<br />
** Created a new EMSegmenter Tutorial (simple mode) - (for quick results, no need to change parameters, this will be useful to clinicians)<br />
** Created a new EMSegmenter Tutorial (advanced mode) - for experienced user of the EMSegmenter<br />
** Created the new 'MRI Human Brain Parcellation' pipeline and added to 3D Slicer 3.6.2 (collaborators: Padmapriya Srinivasan and Sylvain Bouix, PNL BWH)<br />
* 11/12/10<br />
** Restructuring EMSegmenter's Tasks folder to support multiple pipelines<br />
** Start working on a 'MRI Human Brain Parcellation' pipeline (collaborators: Padmapriya Srinivasan and Sylvain Bouix, PNL BWH)<br />
** Start working on a 'Non Human Primate' pipeline (collaborators: Andriy Fedorov, BWH)<br />
** Slicer 3.6.2-RC2 maintenance<br />
* 11/05/10<br />
** software testing for Slicer 3.6.2 release<br />
** Added new test for option --intermediateResultsDirectory<br />
** Fixed bug 1023: MRML import doesn't read copied mrml scenes reliable<br />
** Fixed bug 1025: Slicer crashes when BRAINSFit returns error<br />
* 10/29/10<br />
** Pop up error message when performing segmentation<br />
** Add CMTK in Generic.tcl <br />
** BUG: use .mat extension for transformation files" GenericTask.tcl<br />
** Bug fixing with Slicer Base Code developers<br />
* 10/23/10<br />
** Bug fixes for Slicer 3.6.2 release<br />
** Memory leak fixed<br />
** comment-out unused code in MRI-Human-Brain.tcl<br />
* 10/15/10<br />
** Added function for automatically generating Template File <br />
** Added function for downloading task files from web<br />
** Added CMTK to extension module<br />
** One can assign now tcl file when creating a new task<br />
** Added class name to all tabs<br />
** Tested command line<br />
** Created virtual machines to submit tests reports to the dashboard<br />
** Created Popup window when an error message appears in pre-processing and segmentation<br />
** EMSegmenter works now with different image data types (short, float,...)<br />
** Removed several bugs in mrml structure<br />
<br />
* 10/8/10<br />
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory<br />
** Fixed the leaks in the nightly tests<br />
* 10/1/10<br />
** Removed command line nodes from mrml scene after the command line is executed<br />
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine<br />
** Added label - in addition to the tree - to show the selected anatomical tree node<br />
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)<br />
** Working on parallel execution of multiple instances of the EMSegmentCommandLine<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation:PriorityList&diff=62702Projects:ARRA:miAnnotation:PriorityList2010-12-29T01:58:23Z<p>Pohl: /* Slicer4: Annotation module - Priority List for December release */</p>
<hr />
<div>== Slicer4: Annotation module - Priority List for December release ==<br />
<br />
'''This list includes to-be-done features, open issues and other related things to do.''' High and Medium priorities target the December release.<br />
<br />
<font color=red>HIGH</font><br />
# <strike>Scenesnapshot/scene annotation. See [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule here] for an example.</strike><br />
#* <strike>Will integrate functionality in Annotation Module - review existing functionality for saving/loading views and merge it with screenshot in annotation tool</strike><br />
#* <strike>Ron will work with somebody else to create fancy user interface </strike><br />
# '''2D widget interaction'''<br />
#* '''When using the lightbox view the Annotations do not get displayed properly yet, only fiducials work (work in progress by Kitware)'''<br />
#* <strike>When switching slice orientation the Annotations do not get displayed properly yet</strike><br />
#* '''When widget is not displayed completely in an orientation but intersects with the specific slice, show the intersection as a dot (01/14/11)'''<br />
#* <strike>Sometimes after placement of fiducials funky behavior when switching to different widget [dependency: VTK Widget Fiesta 5/6th November 2010]</strike><br />
# <strike>Annotation hierarchies [dependency: QTreeModel by Nicole]</strike><br />
#* <strike>GUI: Nice tree view with functionality to create/delete hierarchies, drag'n'drop annotations, view/edit/(un-)lock/delete annotations</strike><br />
#* <strike>Logic: include an invisible top-level hierarchy, create appropriate hierarchy nodes when annotations are created, properly delete MRML nodes + widgets</strike><br />
# '''Property dialog to set text, line and point properties (01/14/11)'''<br />
#* '''GUI: Align the layout better (01/14/11)'''<br />
#* '''Logic: Update DisplayNode according to settings in dialog and together with hierarchies (01/14/11)'''<br />
# <strike>Generate Report with option to select specific Annotations [dependency: #3]</strike><br />
# <strike>Implement Save/Load MRML Scene with Annotations [dependency: #3, #4]</strike><br />
# <strike>vtkTextWidget [dependency: VTK Widget Fiesta 5/6th November 2010]</strike><br />
#* <strike>Add option to attach text to a specific point in 2D/3D space and ability to configure the line</strike><br />
# '''vtkRulerWidget (work in progress by Kitware)'''<br />
#* '''Show the dividers on a fixed scale according to millimeter or cm'''<br />
# '''Tutorial'''<br />
<br />
<font color=orange>MEDIUM</font><br />
# <strike>Use own file extension to save annotations (Ron)</strike<br />
#* <strike>Ideas: .anot8 (annot-eight) .mian (medical informatics annotation) .sa (slicer annotation) .san (slicer annotation)</strike><br />
#** <strike>.saf (slicer annotation format) .sat (slicer annotation tool) are already taken:[http://www.fileinfo.com/extension/saf 1]</strike><br />
# Add vtkMRMLAnnotationDicomNode to fetch a header from a loaded volume and store it inside the MRML tree (file/add volume has some of that functionality already). (TBD)<br />
# <strike>Implement "reset viewer" button - viewer is returned to setting when annotation was last modified </strike><br />
<br />
<font color=green>LOW</font><br />
# <strike>Add Screenshot functionality for 2D Viewers (maybe directly in Slicer instead?)</strike><br />
# <strike>Add Screenshot and Description Annotations for a new Snapshot module</strike><br />
#* <strike>MRML: Introduce vtkMRMLAnnotationSnapshotNode then vtkMRMLAnnotationDescriptionNode and vtkMRMLAnnotationScreenshotNode to implement functionality</strike><br />
#** <strike>These will not be displayed in the 3D Scene or 2D viewer - only in the new Snapshot module or during loading of scenes as a browser</strike><br />
# Include new Slicer mouse mode toolbox [dependency: Mouse mode toolbox by Wendy]<br />
# <strike>Use the new Widget API to place/interact with widgets [dependency: VTK Widget Fiesta 5/6th November 2010]</strike><br />
# Get-together with Mike Halle to discuss AIM Annotation tools (IPAD, ClearCanvas plugin)<br />
# Replace click-counter by stack to set different mouse icons according to the placement/interaction state of widget<br />
# Automatic alignment of annotations (Ron)<br />
#* example: SPL Atlas java viewer (see screenshot http://wiki.na-mic.org/Wiki/index.php/File:Atlasjavaviewerannotations.png)<br />
# Add a scalar color bar annotation<br />
# Export to AIM language (Ron)<br />
#* See https://cabig.nci.nih.gov/tools/AIM for details<br />
# Adding histology slides as annotations (http://www.youtube.com/user/kitware#p/a/CBEE89D886EBFFBF/0/up9UPM4Wb44) (Ron)<br />
# Make a demo with /data/Dropbox/RonsExamples/NeuroDemoMayExperiments/2010-03-4Views.mrml (Ron)<br />
# Use new LUT created by Michael Halle (Ron)<br />
# Generate more UML diagrams</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation:PriorityList&diff=62701Projects:ARRA:miAnnotation:PriorityList2010-12-29T01:57:42Z<p>Pohl: /* Slicer4: Annotation module - Priority List for December release */</p>
<hr />
<div>== Slicer4: Annotation module - Priority List for December release ==<br />
<br />
'''This list includes to-be-done features, open issues and other related things to do.''' High and Medium priorities target the December release.<br />
<br />
<font color=red>HIGH</font><br />
# <strike>Scenesnapshot/scene annotation. See [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule here] for an example.</strike><br />
#* <strike>Will integrate functionality in Annotation Module - review existing functionality for saving/loading views and merge it with screenshot in annotation tool</strike><br />
#* <strike>Ron will work with somebody else to create fancy user interface </strike><br />
# '''2D widget interaction'''<br />
#* '''When using the lightbox view the Annotations do not get displayed properly yet, only fiducials work (work in progress by Kitware)'''<br />
#* <strike>When switching slice orientation the Annotations do not get displayed properly yet</strike><br />
#* '''When widget is not displayed completely in an orientation but intersects with the specific slice, show the intersection as a dot (01/14/11)'''<br />
#* <strike>Sometimes after placement of fiducials funky behavior when switching to different widget [dependency: VTK Widget Fiesta 5/6th November 2010]</strike><br />
# <strike>Annotation hierarchies [dependency: QTreeModel by Nicole]</strike><br />
#* <strike>GUI: Nice tree view with functionality to create/delete hierarchies, drag'n'drop annotations, view/edit/(un-)lock/delete annotations</strike><br />
#* <strike>Logic: include an invisible top-level hierarchy, create appropriate hierarchy nodes when annotations are created, properly delete MRML nodes + widgets</strike><br />
# '''Property dialog to set text, line and point properties (01/14/11)'''<br />
#* '''GUI: Align the layout better (01/14/11)'''<br />
#* '''Logic: Update DisplayNode according to settings in dialog and together with hierarchies (01/14/11)'''<br />
# <strike>Generate Report with option to select specific Annotations [dependency: #3]</strike><br />
# <strike>Implement Save/Load MRML Scene with Annotations [dependency: #3, #4]</strike><br />
# <strike>vtkTextWidget [dependency: VTK Widget Fiesta 5/6th November 2010]</strike><br />
#* <strike>Add option to attach text to a specific point in 2D/3D space and ability to configure the line</strike><br />
# '''vtkRulerWidget (work in progress by Kitware)'''<br />
#* '''Show the dividers on a fixed scale according to millimeter or cm'''<br />
# Tutorial<br />
<br />
<font color=orange>MEDIUM</font><br />
# <strike>Use own file extension to save annotations (Ron)</strike<br />
#* <strike>Ideas: .anot8 (annot-eight) .mian (medical informatics annotation) .sa (slicer annotation) .san (slicer annotation)</strike><br />
#** <strike>.saf (slicer annotation format) .sat (slicer annotation tool) are already taken:[http://www.fileinfo.com/extension/saf 1]</strike><br />
# Add vtkMRMLAnnotationDicomNode to fetch a header from a loaded volume and store it inside the MRML tree (file/add volume has some of that functionality already). (TBD)<br />
# <strike>Implement "reset viewer" button - viewer is returned to setting when annotation was last modified </strike><br />
<br />
<font color=green>LOW</font><br />
# <strike>Add Screenshot functionality for 2D Viewers (maybe directly in Slicer instead?)</strike><br />
# <strike>Add Screenshot and Description Annotations for a new Snapshot module</strike><br />
#* <strike>MRML: Introduce vtkMRMLAnnotationSnapshotNode then vtkMRMLAnnotationDescriptionNode and vtkMRMLAnnotationScreenshotNode to implement functionality</strike><br />
#** <strike>These will not be displayed in the 3D Scene or 2D viewer - only in the new Snapshot module or during loading of scenes as a browser</strike><br />
# Include new Slicer mouse mode toolbox [dependency: Mouse mode toolbox by Wendy]<br />
# <strike>Use the new Widget API to place/interact with widgets [dependency: VTK Widget Fiesta 5/6th November 2010]</strike><br />
# Get-together with Mike Halle to discuss AIM Annotation tools (IPAD, ClearCanvas plugin)<br />
# Replace click-counter by stack to set different mouse icons according to the placement/interaction state of widget<br />
# Automatic alignment of annotations (Ron)<br />
#* example: SPL Atlas java viewer (see screenshot http://wiki.na-mic.org/Wiki/index.php/File:Atlasjavaviewerannotations.png)<br />
# Add a scalar color bar annotation<br />
# Export to AIM language (Ron)<br />
#* See https://cabig.nci.nih.gov/tools/AIM for details<br />
# Adding histology slides as annotations (http://www.youtube.com/user/kitware#p/a/CBEE89D886EBFFBF/0/up9UPM4Wb44) (Ron)<br />
# Make a demo with /data/Dropbox/RonsExamples/NeuroDemoMayExperiments/2010-03-4Views.mrml (Ron)<br />
# Use new LUT created by Michael Halle (Ron)<br />
# Generate more UML diagrams</div>Pohlhttps://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=60167EngineeringRetreat20102010-11-02T00:40:19Z<p>Pohl: /* Slicer 4 */</p>
<hr />
<div> [[Events|Back to Events]]<br />
<br />
'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br />
=Logistics=<br />
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br />
* Where: Boston SPL, 1249 Facility<br />
* Who: Engineering Core leaders and key personnel<br />
* Hotel: Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, Massachusetts 02142, Phone: 1-617-494-6600<br />
<br />
=Strategy=<br />
* Slicer 3.6.x is in maintenance mode.<br />
* New development efforts are targeted at Slicer 4. <br />
* Communication with "Customers" is a top priority.<br />
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br />
** For end-users: simplify the user interface, streamline and simplify common workflows<br />
** Support the development of solutions<br />
** We are '''not''' in the "early adopter game" for the next two years<br />
<br />
==Short term goals==<br />
* Targeted for AHM<br />
* Assign owners for each bullet item on this list<br />
===Slicer 3===<br />
*stabilize and [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues debug Slicer 3.6]<br />
*stabilize and document extensions and the process leading to them<br />
<br />
===Slicer 4===<br />
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br />
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br />
** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)<br />
* Rons number 2: Make load/save easier to understand for new users.<br />
** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog]. <br />
** Plan and implement minimalist UI design for load<br />
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br />
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br />
* Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br />
* Implement and package up module templates for developers of interactive modules to get a jump on consistent UXP.(wjp)<br />
* Refine design of slice viewer's control panel to make more compact and quiet. (wjp)<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule Scene module]: A new module to organize scenes and scenesnapshots <br />
* Update Wiki pages:<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br />
* Create a XML Schema for .mrml to check if a mrml document is 'well-formed' and 'valid'. Automatic generated (error free) parser can then be used for accessing/editing mrml files.<br />
* Bug patches from Slicer 3.6 to Slicer 4<br />
<br />
=== Requests from the DBPs ===<br />
==== Utah ====<br />
==== Iowa ====<br />
==== UCLA ====<br />
* [http://trackvis.org/docs/?subsect=fileformat trackvis file format interoperability]<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/20206274 NIfTI DWI file format interoperability] [http://mind.loni.ucla.edu/specification/overview/ LONI MiND Framework]<br />
<br />
==== MGH ====<br />
<br />
== Longer Term Goals ==<br />
* DICOM read and write (local and remote) via CTK<br />
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br />
* Organizing multiple data sets from one subject: time series, image fusion etc.<br />
* Packaging/Superbuild fixes<br />
** Package for linux<br />
** Windows - clean registry on uninstall<br />
** Mac - .dmg into application folder<br />
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br />
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br />
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br />
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br />
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4<br />
** Review Slicer application framework to support modularization and customization<br />
** Two audiences:<br />
*** Create new GUI infrastructure where a simple Interface is created for each application area, e.g. one GUI for Radiologists reading brain MRI, another one for torso CT, ...<br />
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br />
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br />
* Switch to client/server dashboards and take advantage of its benefits<br />
** Each night binaries copied from client machines to Dashboard page/database that manages them<br />
** Ensures Dashboards, builds, releases using common tags/svn#s<br />
** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br />
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")<br />
* GUI Testing<br />
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br />
* Support scenes containing data that spans multiple scales in time and space<br />
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br />
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br />
* Guidelines and examples for GPU-based algorithms<br />
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br />
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br />
* Batch processing (IPython) examples<br />
** includes an algorithm validation framework<br />
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br />
* Consider ITKv4 module management tools being developed (after they have been released as stable release)<br />
** Documentation prior to code development<br />
** Module-specific dashboards<br />
** forum-style commentaries on modules<br />
* Improve support of Windows platform <br />
** Simplify compilation of Slicer on Windows Machines <br />
** Increase speed and stability of Slicer on Windows Machines<br />
* Change release policy: A Slicer release version must not use/depend on ITK Review. If we do not make this modification then we cannot release Slicer as Debian package anymore.<br />
<br />
=Agenda=<br />
<br />
=See also=<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br />
<br />
=Attendees=<br />
#Steve Pieper<br />
#Will Schroeder<br />
#Jim Miller<br />
#Ron Kikinis</div>Pohlhttps://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=60130EngineeringRetreat20102010-11-01T17:15:01Z<p>Pohl: /* Longer Term Goals */</p>
<hr />
<div> [[Events|Back to Events]]<br />
<br />
'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br />
=Logistics=<br />
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br />
* Where: Boston SPL, 1249 Facility<br />
* Who: Engineering Core leaders and key personnel<br />
* Hotel: Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, Massachusetts 02142, Phone: 1-617-494-6600<br />
<br />
=Strategy=<br />
* Slicer 3.6.x is in maintenance mode.<br />
* New development efforts are targeted at Slicer 4. <br />
* Communication with "Customers" is a top priority.<br />
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br />
** For end-users: simplify the user interface, streamline and simplify common workflows<br />
** Support the development of solutions<br />
** We are '''not''' in the "early adopter game" for the next two years<br />
<br />
==Short term goals==<br />
* Targeted for AHM<br />
* Assign owners for each bullet item on this list<br />
===Slicer 3===<br />
*stabilize and [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues debug Slicer 3.6]<br />
*stabilize and document extensions and the process leading to them<br />
<br />
===Slicer 4===<br />
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br />
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br />
** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)<br />
* Rons number 2: Make load/save easier to understand for new users.<br />
** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog]. <br />
** Plan and implement minimalist UI design for load<br />
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br />
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br />
* Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br />
* Implement and package up module templates for developers of interactive modules to get a jump on consistent UXP.(wjp)<br />
* Refine design of slice viewer's control panel to make more compact and quiet. (wjp)<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule Scene module]: A new module to organize scenes and scenesnapshots <br />
* Update Wiki pages:<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br />
* Create a XML Schema for .mrml to check if a mrml document is 'well-formed' and 'valid'. Automatic generated (error free) parser can then be used for accessing/editing mrml files.<br />
<br />
=== Requests from the DBPs ===<br />
==== Utah ====<br />
==== Iowa ====<br />
==== UCLA ====<br />
* [http://trackvis.org/docs/?subsect=fileformat trackvis file format interoperability]<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/20206274 NIfTI DWI file format interoperability]<br />
==== MGH ====<br />
<br />
== Longer Term Goals ==<br />
* DICOM read and write (local and remote) via CTK<br />
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br />
* Organizing multiple data sets from one subject: time series, image fusion etc.<br />
* Packaging/Superbuild fixes<br />
** Package for linux<br />
** Windows - clean registry on uninstall<br />
** Mac - .dmg into application folder<br />
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br />
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br />
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br />
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br />
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4<br />
** Review Slicer application framework to support modularization and customization<br />
** Two audiences:<br />
*** Create new GUI infrastructure where a simple Interface is created for each application area, e.g. one GUI for Radiologists reading brain MRI, another one for torso CT, ...<br />
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br />
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br />
* Switch to client/server dashboards and take advantage of its benefits<br />
** Each night binaries copied from client machines to Dashboard page/database that manages them<br />
** Ensures Dashboards, builds, releases using common tags/svn#s<br />
** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br />
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")<br />
* GUI Testing<br />
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br />
* Support scenes containing data that spans multiple scales in time and space<br />
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br />
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br />
* Guidelines and examples for GPU-based algorithms<br />
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br />
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br />
* Batch processing (IPython) examples<br />
** includes an algorithm validation framework<br />
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br />
* Consider ITKv4 module management tools being developed (after they have been released as stable release)<br />
** Documentation prior to code development<br />
** Module-specific dashboards<br />
** forum-style commentaries on modules<br />
* Improve support of Windows platform <br />
** Simplify compilation of Slicer on Windows Machines <br />
** Increase speed and stability of Slicer on Windows Machines<br />
* Change release policy: A Slicer release version must not use/depend on ITK Review. If we do not make this modification then we cannot release Slicer as Debian package anymore.<br />
<br />
=Agenda=<br />
<br />
=See also=<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br />
<br />
=Attendees=<br />
#Steve Pieper<br />
#Will Schroeder<br />
#Jim Miller<br />
#Ron Kikinis</div>Pohlhttps://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=60129EngineeringRetreat20102010-11-01T17:13:16Z<p>Pohl: /* Slicer 4 */</p>
<hr />
<div> [[Events|Back to Events]]<br />
<br />
'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br />
=Logistics=<br />
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br />
* Where: Boston SPL, 1249 Facility<br />
* Who: Engineering Core leaders and key personnel<br />
* Hotel: Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, Massachusetts 02142, Phone: 1-617-494-6600<br />
<br />
=Strategy=<br />
* Slicer 3.6.x is in maintenance mode.<br />
* New development efforts are targeted at Slicer 4. <br />
* Communication with "Customers" is a top priority.<br />
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br />
** For end-users: simplify the user interface, streamline and simplify common workflows<br />
** Support the development of solutions<br />
** We are '''not''' in the "early adopter game" for the next two years<br />
<br />
==Short term goals==<br />
* Targeted for AHM<br />
* Assign owners for each bullet item on this list<br />
===Slicer 3===<br />
*stabilize and [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues debug Slicer 3.6]<br />
*stabilize and document extensions and the process leading to them<br />
<br />
===Slicer 4===<br />
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br />
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br />
** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)<br />
* Rons number 2: Make load/save easier to understand for new users.<br />
** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog]. <br />
** Plan and implement minimalist UI design for load<br />
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br />
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br />
* Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br />
* Implement and package up module templates for developers of interactive modules to get a jump on consistent UXP.(wjp)<br />
* Refine design of slice viewer's control panel to make more compact and quiet. (wjp)<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule Scene module]: A new module to organize scenes and scenesnapshots <br />
* Update Wiki pages:<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br />
* Create a XML Schema for .mrml to check if a mrml document is 'well-formed' and 'valid'. Automatic generated (error free) parser can then be used for accessing/editing mrml files.<br />
<br />
=== Requests from the DBPs ===<br />
==== Utah ====<br />
==== Iowa ====<br />
==== UCLA ====<br />
* [http://trackvis.org/docs/?subsect=fileformat trackvis file format interoperability]<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/20206274 NIfTI DWI file format interoperability]<br />
==== MGH ====<br />
<br />
== Longer Term Goals ==<br />
* DICOM read and write (local and remote) via CTK<br />
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br />
* Organizing multiple data sets from one subject: time series, image fusion etc.<br />
* Packaging/Superbuild fixes<br />
** Package for linux<br />
** Windows - clean registry on uninstall<br />
** Mac - .dmg into application folder<br />
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br />
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br />
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br />
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br />
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4<br />
** Review Slicer application framework to support modularization and customization<br />
** Two audiences:<br />
*** Create new GUI infrastructure where a simple Interface is created for each application area, e.g. one GUI for Radiologists reading brain MRI, another one for torso CT, ...<br />
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br />
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br />
* Switch to client/server dashboards and take advantage of its benefits<br />
** Each night binaries copied from client machines to Dashboard page/database that manages them<br />
** Ensures Dashboards, builds, releases using common tags/svn#s<br />
** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br />
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")<br />
* GUI Testing<br />
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br />
* Support scenes containing data that spans multiple scales in time and space<br />
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br />
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br />
* Guidelines and examples for GPU-based algorithms<br />
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br />
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br />
* Batch processing (IPython) examples<br />
** includes an algorithm validation framework<br />
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br />
* Consider ITKv4 module management tools being developed (after they have been released as stable release)<br />
** Documentation prior to code development<br />
** Module-specific dashboards<br />
** forum-style commentaries on modules<br />
* Improve support of Windows platform <br />
** Simplify compilation of Slicer on Windows Machines <br />
** Increase speed and stability of Slicer on Windows Machines<br />
<br />
=Agenda=<br />
<br />
=See also=<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br />
<br />
=Attendees=<br />
#Steve Pieper<br />
#Will Schroeder<br />
#Jim Miller<br />
#Ron Kikinis</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=60037Projects:ARRA:SlicerEM2010-10-30T17:01:47Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 10/29/10<br />
** Pop up error message when performing segmentation<br />
** Add CMTK in Generic.tcl <br />
** BUG: use .mat extension for transformation files" GenericTask.tcl<br />
** Bug fixing with Slicer Base Code developers<br />
* 10/23/10<br />
** Bug fixes for Slicer 3.6.2 release<br />
** Memory leak fixed<br />
** comment-out unused code in MRI-Human-Brain.tcl<br />
* 10/15/10<br />
** Added function for automatically generating Template File <br />
** Added function for downloading task files from web<br />
** Added CMTK to extension module<br />
** One can assign now tcl file when creating a new task<br />
** Added class name to all tabs<br />
** Tested command line<br />
** Created virtual machines to submit tests reports to the dashboard<br />
** Created Popup window when an error message appears in pre-processing and segmentation<br />
** EMSegmenter works now with different image data types (short, float,...)<br />
** Removed several bugs in mrml structure<br />
<br />
* 10/8/10<br />
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory<br />
** Fixed the leaks in the nightly tests<br />
* 10/1/10<br />
** Removed command line nodes from mrml scene after the command line is executed<br />
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine<br />
** Added label - in addition to the tree - to show the selected anatomical tree node<br />
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)<br />
** Working on parallel execution of multiple instances of the EMSegmentCommandLine<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation:PriorityList&diff=59698Projects:ARRA:miAnnotation:PriorityList2010-10-25T20:10:37Z<p>Pohl: /* Slicer4: Annotation module - Priority List for December release */</p>
<hr />
<div>== Slicer4: Annotation module - Priority List for December release ==<br />
<br />
'''This list includes to-be-done features, open issues and other related things to do.''' High and Medium priorities target the December release.<br />
<br />
<font color=red>HIGH</font><br />
# Scenesnapshot/scene annotation. See [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule here] for an example.<br />
#* Will integrate functionality in Annotation Module - review existing functionality for saving/loading views and merge it with screenshot in annotation tool<br />
#* Ron will work with somebody else to create fancy user interface <br />
# 2D widget interaction<br />
#* When using the lightbox view the Annotations do not get displayed properly yet<br />
#* When switching slice orientation the Annotations do not get displayed properly yet<br />
#* When widget is not displayed completely in an orientation but intersects with the specific slice, show the intersection as a dot<br />
#* Sometimes after placement of fiducials funky behavior when switching to different widget<br />
# Annotation hierarchies [dependency: QTreeModel by Nicole]<br />
#* GUI: Nice tree view with functionality to create/delete hierarchies, drag'n'drop annotations, view/edit/(un-)lock/delete annotations<br />
#* Logic: include an invisible top-level hierarchy, create appropriate hierarchy nodes when annotations are created, properly delete MRML nodes + widgets<br />
# Property dialog to set text, line and point properties [dependency: #2]<br />
#* GUI: Align the layout better<br />
#* Logic: Update DisplayNode according to settings in dialog and together with hierarchies<br />
# Generate Report with option to select specific Annotations [dependency: #2]<br />
# Implement Save/Load MRML Scene with Annotations [dependency: #2, #3]<br />
# vtkTextWidget [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
#* Add option to attach text to a specific point in 2D/3D space and ability to configure the line<br />
# vtkRulerWidget [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
#* Show the dividers on a fixed scale according to millimeter or cm<br />
<br />
<font color=orange>MEDIUM</font><br />
# Use own file extension to save annotations (Ron)<br />
#* Ideas: .anot8 (annot-eight) .saf (slicer annotation format) .sat (slicer annotation tool), .mian (medical informatics annotation), but check if they are taken:[http://www.fileinfo.com/extension/saf 1]<br />
# Add vtkMRMLAnnotationDicomNode to fetch a header from a loaded volume and store it inside the MRML tree (file/add volume has some of that functionality already).<br />
# Implement "reset viewer" button - viewer is returned to setting when annotation was last modified <br />
<br />
<font color=green>LOW</font><br />
# Add Screenshot functionality for 2D Viewers (maybe directly in Slicer instead?)<br />
# Add Screenshot and Description Annotations for a new Snapshot module<br />
#* MRML: Introduce vtkMRMLAnnotationSnapshotNode then vtkMRMLAnnotationDescriptionNode and vtkMRMLAnnotationScreenshotNode to implement functionality<br />
#** These will not be displayed in the 3D Scene or 2D viewer - only in the new Snapshot module or during loading of scenes as a browser<br />
# Include new Slicer mouse mode toolbox [dependency: Mouse mode toolbox by Wendy]<br />
# Use the new Widget API to place/interact with widgets [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
# Get-together with Mike Halle to discuss AIM Annotation tools (IPAD, ClearCanvas plugin)<br />
# Replace click-counter by stack to set different mouse icons according to the placement/interaction state of widget<br />
# Automatic alignment of annotations (Ron)<br />
#* example: SPL Atlas java viewer (see screenshot http://wiki.na-mic.org/Wiki/index.php/File:Atlasjavaviewerannotations.png)<br />
# Add a scalar color bar annotation<br />
# Export to AIM language (Ron)<br />
#* See https://cabig.nci.nih.gov/tools/AIM for details<br />
# Adding histology slides as annotations (http://www.youtube.com/user/kitware#p/a/CBEE89D886EBFFBF/0/up9UPM4Wb44) (Ron)<br />
# Make a demo with /data/Dropbox/RonsExamples/NeuroDemoMayExperiments/2010-03-4Views.mrml (Ron)<br />
# Use new LUT created by Michael Halle (Ron)<br />
# Generate more UML diagrams</div>Pohlhttps://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=59679EngineeringRetreat20102010-10-25T18:29:35Z<p>Pohl: /* Longer Term Goals */</p>
<hr />
<div> [[Events|Back to Events]]<br />
<br />
'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br />
=Logistics=<br />
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br />
* Where: Boston SPL, 1249 Facility<br />
* Who: Engineering Core leaders and key personnel<br />
<br />
=Strategy=<br />
* Slicer 3.6.x is in maintenance mode.<br />
* New development efforts are targeted at Slicer 4. <br />
* Communication with "Customers" is a top priority.<br />
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br />
** For end-users: simplify the user interface, streamline and simplify common workflows<br />
** Support the development of solutions<br />
** We are '''not''' in the early adopter game for the next two years<br />
<br />
==Short term goals==<br />
* Targeted for AHM<br />
* Assign owners for each bullet item on this list<br />
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br />
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br />
** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)<br />
* Rons number 2: Make load/save easier to understand for new users.<br />
** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog]. <br />
** Plan and implement minimalist UI design for load<br />
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br />
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br />
* Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:SceneModule Scene module]: A new module to organize scenes and scenesnapshots <br />
* Update Wiki pages:<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br />
<br />
== Longer Term Goals ==<br />
* DICOM read and write (local and remote) via CTK<br />
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br />
* Organizing multiple data sets from one subject: time series, image fusion etc.<br />
* Packaging/Superbuild fixes<br />
** Package for linux<br />
** Windows - clean registry on uninstall<br />
** Mac - .dmg into application folder<br />
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br />
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br />
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br />
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br />
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4<br />
** Review Slicer application framework to support modularization and customization<br />
** Two audiences:<br />
*** Create new GUI infrastructure where a simple Interface is created for each application area, e.g. one GUI for Radiologists reading brain MRI, another one for torso CT, ...<br />
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br />
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br />
* Switch to client/server dashboards and take advantage of its benefits<br />
** Each night binaries copied from client machines to Dashboard page/database that manages them<br />
** Ensures Dashboards, builds, releases using common tags/svn#s<br />
** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br />
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")<br />
* GUI Testing<br />
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br />
* Support scenes containing data that spans multiple scales in time and space<br />
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br />
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br />
* Guidelines and examples for GPU-based algorithms<br />
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br />
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br />
* Batch processing (IPython) examples<br />
** includes an algorithm validation framework<br />
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br />
* Consider ITKv4 module management tools being developed (after they have been released as stable release)<br />
** Documentation prior to code development<br />
** Module-specific dashboards<br />
** forum-style commentaries on modules<br />
* Improve support of Windows platform <br />
** Simplify compilation of Slicer on Windows Machines <br />
** Increase speed and stability of Slicer on Windows Machines<br />
<br />
=Agenda=<br />
<br />
=See also=<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br />
<br />
=Attendees=<br />
#Steve Pieper<br />
#Will Schroeder<br />
#Jim Miller<br />
#Ron Kikinis</div>Pohlhttps://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=59676EngineeringRetreat20102010-10-25T18:23:35Z<p>Pohl: /* Longer Term Goals */</p>
<hr />
<div> [[Events|Back to Events]]<br />
<br />
'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br />
=Logistics=<br />
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br />
* Where: Boston SPL, 1249 Facility<br />
* Who: Engineering Core leaders and key personnel<br />
<br />
=Strategy=<br />
* Slicer 3.6.x is in maintenance mode.<br />
* New development efforts are targeted at Slicer 4. <br />
* Communication with "Customers" is a top priority.<br />
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br />
** For end-users: simplify the user interface, streamline and simplify common workflows<br />
** Support the development of solutions<br />
** We are '''not''' in the early adopter game for the next two years<br />
<br />
==Short term goals==<br />
* Targeted for AHM<br />
* Assign owners for each bullet item on this list<br />
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br />
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br />
** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)<br />
* Rons number 2: Make load/save easier to understand for new users.<br />
** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog]. <br />
** Plan and implement minimalist UI design for load<br />
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br />
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br />
* Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br />
* Scene module: reorder, rename (Wendy)<br />
* Update Wiki pages:<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br />
<br />
== Longer Term Goals ==<br />
* DICOM read and write (local and remote) via CTK<br />
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br />
* Organizing multiple data sets from one subject: time series, image fusion etc.<br />
* Packaging/Superbuild fixes<br />
** Package for linux<br />
** Windows - clean registry on uninstall<br />
** Mac - .dmg into application folder<br />
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br />
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br />
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br />
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br />
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4<br />
** Review Slicer application framework to support modularization and customization<br />
** Two audiences:<br />
*** Simple Interface infrastructure that adopts to specific tasks, such as for Radiologists reading brain MRI , another one for torso CT, ...<br />
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br />
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br />
* Switch to client/server dashboards and take advantage of its benefits<br />
** Each night binaries copied from client machines to Dashboard page/database that manages them<br />
** Ensures Dashboards, builds, releases using common tags/svn#s<br />
** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br />
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")<br />
* GUI Testing<br />
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br />
* Support scenes containing data that spans multiple scales in time and space<br />
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br />
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br />
* Guidelines and examples for GPU-based algorithms<br />
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br />
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br />
* Batch processing (IPython) examples<br />
** includes an algorithm validation framework<br />
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br />
* Consider ITKv4 module management tools being developed (after they have been released as stable release)<br />
** Documentation prior to code development<br />
** Module-specific dashboards<br />
** forum-style commentaries on modules<br />
* Improve support of Windows platform <br />
** Simplify compilation of Slicer on Windows Machines <br />
** Increase speed and stability of Slicer on Windows Machines<br />
<br />
=Agenda=<br />
<br />
=See also=<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br />
<br />
=Attendees=<br />
#Steve Pieper<br />
#Will Schroeder<br />
#Jim Miller<br />
#Ron Kikinis</div>Pohlhttps://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=59675EngineeringRetreat20102010-10-25T18:22:38Z<p>Pohl: /* Longer Term Goals */</p>
<hr />
<div> [[Events|Back to Events]]<br />
<br />
'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br />
=Logistics=<br />
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br />
* Where: Boston SPL, 1249 Facility<br />
* Who: Engineering Core leaders and key personnel<br />
<br />
=Strategy=<br />
* Slicer 3.6.x is in maintenance mode.<br />
* New development efforts are targeted at Slicer 4. <br />
* Communication with "Customers" is a top priority.<br />
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br />
** For end-users: simplify the user interface, streamline and simplify common workflows<br />
** Support the development of solutions<br />
** We are '''not''' in the early adopter game for the next two years<br />
<br />
==Short term goals==<br />
* Targeted for AHM<br />
* Assign owners for each bullet item on this list<br />
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br />
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br />
** [[Projects:ARRA:miAnnotation:PriorityList|Annotation]]: User-provided description of scenesnapshot/scene (Daniel Haehn)<br />
* Rons number 2: Make load/save easier to understand for new users.<br />
** Single interface to all data sources based on [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png QSlicerVolumesIODialog]. <br />
** Plan and implement minimalist UI design for load<br />
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br />
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br />
* Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br />
* Scene module: reorder, rename (Wendy)<br />
* Update Wiki pages:<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br />
<br />
== Longer Term Goals ==<br />
* DICOM read and write (local and remote) via CTK<br />
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br />
* Organizing multiple data sets from one subject: time series, image fusion etc.<br />
* Packaging/Superbuild fixes<br />
** Package for linux<br />
** Windows - clean registry on uninstall<br />
** Mac - .dmg into application folder<br />
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br />
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br />
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br />
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br />
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4<br />
** Review Slicer application framework to support modularization and customization<br />
** Two audiences:<br />
*** Simple Interface infrastructure that adopts to specific tasks, such as for Radiologists<br />
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br />
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br />
* Switch to client/server dashboards and take advantage of its benefits<br />
** Each night binaries copied from client machines to Dashboard page/database that manages them<br />
** Ensures Dashboards, builds, releases using common tags/svn#s<br />
** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br />
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")<br />
* GUI Testing<br />
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br />
* Support scenes containing data that spans multiple scales in time and space<br />
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br />
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br />
* Guidelines and examples for GPU-based algorithms<br />
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br />
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br />
* Batch processing (IPython) examples<br />
** includes an algorithm validation framework<br />
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br />
* Consider ITKv4 module management tools being developed (after they have been released as stable release)<br />
** Documentation prior to code development<br />
** Module-specific dashboards<br />
** forum-style commentaries on modules<br />
* Improve support of Windows platform <br />
** Simplify compilation of Slicer on Windows Machines <br />
** Increase speed and stability of Slicer on Windows Machines<br />
<br />
=Agenda=<br />
<br />
=See also=<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br />
<br />
=Attendees=<br />
#Steve Pieper<br />
#Will Schroeder<br />
#Jim Miller<br />
#Ron Kikinis</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation:PriorityList&diff=59633Projects:ARRA:miAnnotation:PriorityList2010-10-25T14:45:19Z<p>Pohl: /* Slicer4: Annotation module - Priority List for December release */</p>
<hr />
<div>== Slicer4: Annotation module - Priority List for December release ==<br />
<br />
'''This list includes to-be-done features, open issues and other related things to do.''' High and Medium priorities target the December release.<br />
<br />
<font color=red>HIGH</font><br />
# 2D widget interaction<br />
#* When using the lightbox view the Annotations do not get displayed properly yet<br />
#* When switching slice orientation the Annotations do not get displayed properly yet<br />
#* When widget is not displayed completely in an orientation but intersects with the specific slice, show the intersection as a dot<br />
#* Sometimes after placement of fiducials funky behavior when switching to different widget<br />
# Annotation hierarchies [dependency: QTreeModel by Nicole]<br />
#* GUI: Nice tree view with functionality to create/delete hierarchies, drag'n'drop annotations, view/edit/(un-)lock/delete annotations<br />
#* Logic: include an invisible top-level hierarchy, create appropriate hierarchy nodes when annotations are created, properly delete MRML nodes + widgets<br />
# Property dialog to set text, line and point properties [dependency: #2]<br />
#* GUI: Align the layout better<br />
#* Logic: Update DisplayNode according to settings in dialog and together with hierarchies<br />
# Generate Report with option to select specific Annotations [dependency: #2]<br />
# Implement Save/Load MRML Scene with Annotations [dependency: #2, #3]<br />
# vtkTextWidget [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
#* Add option to attach text to a specific point in 2D/3D space and ability to configure the line<br />
# vtkRulerWidget [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
#* Show the dividers on a fixed scale according to millimeter or cm<br />
<br />
<font color=orange>MEDIUM</font><br />
# Use own file extension to save annotations (Ron)<br />
#* Ideas: .anot8 (annot-eight) .saf (slicer annotation format) .sat (slicer annotation tool)<br />
# Add vtkMRMLAnnotationDicomNode to fetch a header from a loaded volume and store it inside the MRML tree<br />
# Implement "reset viewer" button - viewer is returned to setting when annotation was last modified <br />
<br />
<font color=green>LOW</font><br />
# Add Screenshot functionality for 2D Viewers (maybe directly in Slicer instead?)<br />
# Add Screenshot and Description Annotations for a new Snapshot module<br />
#* MRML: Introduce vtkMRMLAnnotationSnapshotNode then vtkMRMLAnnotationDescriptionNode and vtkMRMLAnnotationScreenshotNode to implement functionality<br />
#** These will not be displayed in the 3D Scene or 2D viewer - only in the new Snapshot module or during loading of scenes as a browser<br />
# Include new Slicer mouse mode toolbox [dependency: Mouse mode toolbox by Wendy]<br />
# Use the new Widget API to place/interact with widgets [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
# Get-together with Mike Halle to discuss AIM Annotation tools (IPAD, ClearCanvas plugin)<br />
# Replace click-counter by stack to set different mouse icons according to the placement/interaction state of widget<br />
# Automatic alignment of annotations (Ron)<br />
#* example: SPL Atlas java viewer (see screenshot http://wiki.na-mic.org/Wiki/index.php/File:Atlasjavaviewerannotations.png)<br />
# Add a scalar color bar annotation<br />
# Export to AIM language (Ron)<br />
#* See https://cabig.nci.nih.gov/tools/AIM for details<br />
# Adding histology slides as annotations (http://www.youtube.com/user/kitware#p/a/CBEE89D886EBFFBF/0/up9UPM4Wb44) (Ron)<br />
# Make a demo with /data/Dropbox/RonsExamples/NeuroDemoMayExperiments/2010-03-4Views.mrml (Ron)<br />
# Use new LUT created by Michael Halle (Ron)<br />
# Generate more UML diagrams</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:miAnnotation:PriorityList&diff=59632Projects:ARRA:miAnnotation:PriorityList2010-10-25T14:44:13Z<p>Pohl: /* Slicer4: Annotation module - Priority List for December release */</p>
<hr />
<div>== Slicer4: Annotation module - Priority List for December release ==<br />
<br />
'''This list includes to-be-done features, open issues and other related things to do.''' High and Medium priorities target the December release.<br />
<br />
<font color=red>HIGH</font><br />
# 2D widget interaction<br />
#* When using the lightbox view the Annotations do not get displayed properly yet<br />
#* When switching slice orientation the Annotations do not get displayed properly yet<br />
#* When widget is not displayed completely in an orientation but intersects with the specific slice, show the intersection as a dot<br />
#* Sometimes after placement of fiducials funky behavior when switching to different widget<br />
# Annotation hierarchies [dependency: QTreeModel by Nicole]<br />
#* GUI: Nice tree view with functionality to create/delete hierarchies, drag'n'drop annotations, view/edit/(un-)lock/delete annotations<br />
#* Logic: include an invisible top-level hierarchy, create appropriate hierarchy nodes when annotations are created, properly delete MRML nodes + widgets<br />
# Property dialog to set text, line and point properties [dependency: #2]<br />
#* GUI: Align the layout better<br />
#* Logic: Update DisplayNode according to settings in dialog and together with hierarchies<br />
# Generate Report with option to select specific Annotations [dependency: #2]<br />
# Implement Save/Load MRML Scene with Annotations [dependency: #2, #3]<br />
# vtkTextWidget [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
#* Add option to attach text to a specific point in 2D/3D space and ability to configure the line<br />
# vtkRulerWidget [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
#* Show the dividers on a fixed scale according to millimeter or cm<br />
<br />
<font color=orange>MEDIUM</font><br />
# Use own file extension to save annotations (Ron)<br />
#* Ideas: .anot8 (annot-eight) .saf (slicer annotation format) .sat (slicer annotation tool)<br />
# Add vtkMRMLAnnotationDicomNode to fetch a header from a loaded volume and store it inside the MRML tree<br />
# Add Screenshot functionality for 2D Viewers (maybe directly in Slicer instead?)<br />
# Implement "reset viewer" button - viewer is returned to setting when annotation was last modified <br />
<br />
<font color=green>LOW</font><br />
# Add Screenshot and Description Annotations for a new Snapshot module<br />
#* MRML: Introduce vtkMRMLAnnotationSnapshotNode then vtkMRMLAnnotationDescriptionNode and vtkMRMLAnnotationScreenshotNode to implement functionality<br />
#** These will not be displayed in the 3D Scene or 2D viewer - only in the new Snapshot module or during loading of scenes as a browser<br />
# Include new Slicer mouse mode toolbox [dependency: Mouse mode toolbox by Wendy]<br />
# Use the new Widget API to place/interact with widgets [dependency: VTK Widget Fiesta 5/6th November 2010]<br />
# Get-together with Mike Halle to discuss AIM Annotation tools (IPAD, ClearCanvas plugin)<br />
# Replace click-counter by stack to set different mouse icons according to the placement/interaction state of widget<br />
# Automatic alignment of annotations (Ron)<br />
#* example: SPL Atlas java viewer (see screenshot http://wiki.na-mic.org/Wiki/index.php/File:Atlasjavaviewerannotations.png)<br />
# Add a scalar color bar annotation<br />
# Export to AIM language (Ron)<br />
#* See https://cabig.nci.nih.gov/tools/AIM for details<br />
# Adding histology slides as annotations (http://www.youtube.com/user/kitware#p/a/CBEE89D886EBFFBF/0/up9UPM4Wb44) (Ron)<br />
# Make a demo with /data/Dropbox/RonsExamples/NeuroDemoMayExperiments/2010-03-4Views.mrml (Ron)<br />
# Use new LUT created by Michael Halle (Ron)<br />
# Generate more UML diagrams</div>Pohlhttps://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=59626EngineeringRetreat20102010-10-25T13:19:28Z<p>Pohl: /* Longer Term Goals */</p>
<hr />
<div> [[Events|Back to Events]]<br />
<br />
'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br />
=Logistics=<br />
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br />
* Where: Boston SPL, 1249 Facility<br />
* Who: Engineering Core leaders and key personnel<br />
<br />
=Strategy=<br />
* Slicer 3.6.x is in maintenance mode.<br />
* New development efforts are targeted at Slicer 4. <br />
* Communication with "Customers" is a top priority.<br />
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br />
** For end-users: simplify the user interface, streamline and simplify common workflows<br />
** Support the development of solutions<br />
** We are '''not''' in the early adopter game for the next two years<br />
<br />
==Short term goals==<br />
* Targeted for AHM<br />
* Assign owners for each bullet item on this list<br />
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br />
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br />
** Annotation: User-provided description of scenesnapshot/scene (Daniel Haehn)<br />
* Rons number 2: Make load/save easier to understand for new users.<br />
** Single interface to all data sources. <br />
** Plan and implement minimalist UI design for load<br />
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br />
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br />
* Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br />
* Scene snapshot module: reorder, rename (Wendy)<br />
* Update Wiki pages:<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br />
<br />
== Longer Term Goals ==<br />
* DICOM read and write (local and remote) via CTK<br />
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br />
* Organizing multiple data sets from one subject: time series, image fusion etc.<br />
* Packaging/Superbuild fixes<br />
** Package for linux<br />
** Windows - clean registry on uninstall<br />
** Mac - .dmg into application folder<br />
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br />
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br />
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br />
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br />
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4<br />
** Review Slicer application framework to support modularization and customization<br />
** Two audiences:<br />
*** Simple Interface for Radiologists<br />
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br />
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br />
* Switch to client/server dashboards and take advantage of its benefits<br />
** Each night binaries copied from client machines to Dashboard page/database that manages them<br />
** Ensures Dashboards, builds, releases using common tags/svn#s<br />
** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br />
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")<br />
* GUI Testing<br />
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br />
* Support scenes containing data that spans multiple scales in time and space<br />
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br />
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br />
* Guidelines and examples for GPU-based algorithms<br />
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br />
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br />
* Batch processing (IPython) examples<br />
** includes an algorithm validation framework<br />
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br />
* Consider ITKv4 module management tools being developed (after they have been released as stable release)<br />
** Documentation prior to code development<br />
** Module-specific dashboards<br />
** forum-style commentaries on modules<br />
* Improve support of Windows platform <br />
** Simplify compilation of Slicer on Windows Machines <br />
** Increase speed and stability of Slicer on Windows Machines<br />
<br />
=Agenda=<br />
<br />
=See also=<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br />
<br />
=Attendees=<br />
#Steve Pieper<br />
#Will Schroeder<br />
#Jim Miller<br />
#Ron Kikinis</div>Pohlhttps://www.na-mic.org/w/index.php?title=EngineeringRetreat2010&diff=59625EngineeringRetreat20102010-10-25T13:18:38Z<p>Pohl: /* Longer Term Goals */</p>
<hr />
<div> [[Events|Back to Events]]<br />
<br />
'''Goals''': Develop clarity and a plan for this year's work; establish broader strategic vision for the next four NAMIC years.<br />
=Logistics=<br />
* When: November 17-18 (Wednesday and Thursday). Start time: noon Wednesday, end time: early afternoon Thursday<br />
* Where: Boston SPL, 1249 Facility<br />
* Who: Engineering Core leaders and key personnel<br />
<br />
=Strategy=<br />
* Slicer 3.6.x is in maintenance mode.<br />
* New development efforts are targeted at Slicer 4. <br />
* Communication with "Customers" is a top priority.<br />
** For developers: stabilize the Slicer environment. '''Slicer has been a moving target for too long'''.<br />
** For end-users: simplify the user interface, streamline and simplify common workflows<br />
** Support the development of solutions<br />
** We are '''not''' in the early adopter game for the next two years<br />
<br />
==Short term goals==<br />
* Targeted for AHM<br />
* Assign owners for each bullet item on this list<br />
* Rons number 1: Augment scenes and scenesnapshots (see also its counterpart, the [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Download_Data Image Database UI])<br />
** Thumbnails: user selectable toggle: 3d viewer (default), whole frame, red slice viewer, ability to replace thumbnails<br />
** Annotation: User-provided description of scenesnapshot/scene (Daniel Haehn)<br />
* Rons number 2: Make load/save easier to understand for new users.<br />
** Single interface to all data sources. <br />
** Plan and implement minimalist UI design for load<br />
* Rons number 3: Review [http://www.na-mic.org/Bug/view_all_bug_page.php Slicer3 bug tracker] for issues and feature requests - in UI, particular widgets, command line modules, improved transforms/registration... (Steve)<br />
* Rons number 4: Keep [[Projects:ARRA:SlicerUI|Slicer4 Qt port]] on schedule (JF, JC)<br />
* Rons number 5: [[WidgetDesign2010|VTK Widgets Roadmap]] (Will)<br />
* Scene snapshot module: reorder, rename (Wendy)<br />
* Update Wiki pages:<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:CMAKESuperbuild CMAKE superbuild with support for extensions] (Service Core)<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4 Slicer4]<br />
** [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers Slicer4:Developers]<br />
<br />
== Longer Term Goals ==<br />
* DICOM read and write (local and remote) via CTK<br />
* extended save: save to local and remote destinations. Make plans for logic components, DB transaction, and UI design.<br />
* Organizing multiple data sets from one subject: time series, image fusion etc.<br />
* Packaging/Superbuild fixes<br />
** Package for linux<br />
** Windows - clean registry on uninstall<br />
** Mac - .dmg into application folder<br />
* Creation of a [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Display Module]<br />
* Make plans for a new and improved [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor] for slicer4<br />
** Grow Cuts, RSS and fast Marching with volume cropping, integral volume rendering, (limited) GPU acceleration<br />
* Investigate use of a binary mask used with volume rendering to specify non-rectilinear ROIs, to display segmentation results, and to display effects of interactive editing<br />
* Define a "Core" Slicer that can be distributed with InsightApplications repository of ITKv4<br />
** Review Slicer application framework to support modularization and customization<br />
** Two audiences:<br />
*** Simple Interface for Radiologists<br />
*** Simple, Extensible Platform for Developers (for custom apps/interfaces).<br />
* Switch to GIT deferred. Reconsider after the first stable release of Slicer 4.<br />
* Switch to client/server dashboards and take advantage of its benefits<br />
** Each night binaries copied from client machines to Dashboard page/database that manages them<br />
** Ensures Dashboards, builds, releases using common tags/svn#s<br />
** Ensures available binaries include last-successful build, last-release build, and last-nights build.<br />
** Dashboard specifies what should be build on what clients ("CDash@home" or "Client/Server CDash")<br />
* GUI Testing<br />
** There is now an open-source method for automated testing of Qt-based applications: http://www.paraview.org/Wiki/Testing_design<br />
* Support scenes containing data that spans multiple scales in time and space<br />
** visualize, indicate correspondence and support interactions with a scene in which the data differ by orders of magnitude and change over time<br />
* Infrastructure that supports simultaneous GPU-based volume rendering and GPU-based interactive segmentation methods (vtkWidgets)<br />
* Guidelines and examples for GPU-based algorithms<br />
* Interactive/iterative command-line modules (e.g., tied to a vtkWidget)<br />
* Determine an alternative to Mantis/bug-tracking. We have over 495 bugs.<br />
* Batch processing (IPython) examples<br />
** includes an algorithm validation framework<br />
* Interact with [http://www.kitware.com/blog/home/post/49 ITKv4] (once released?), [http://commontk.org CTK], [http://nipy.sourceforge.net/software/projects/ NiPy], and other like-minded projects.<br />
* Consider ITKv4 module management tools being developed (after they have been released as stable release)<br />
** Documentation prior to code development<br />
** Module-specific dashboards<br />
** forum-style commentaries on modules<br />
* Simplify compilation of Slicer on Windows Machines <br />
* Increase speed and stability of Slicer on Windows Machines<br />
<br />
=Agenda=<br />
<br />
=See also=<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4<br />
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Developers<br />
<br />
=Attendees=<br />
#Steve Pieper<br />
#Will Schroeder<br />
#Jim Miller<br />
#Ron Kikinis</div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=59555Projects:ARRA:SlicerEM2010-10-24T00:39:15Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 10/23/10<br />
** Bug fixes for Slicer 3.6.2 release<br />
** Memory leak fixed<br />
** comment-out unused code in MRI-Human-Brain.tcl<br />
* 10/15/10<br />
** Added function for automatically generating Template File <br />
** Added function for downloading task files from web<br />
** Added CMTK to extension module<br />
** One can assign now tcl file when creating a new task<br />
** Added class name to all tabs<br />
** Tested command line<br />
** Created virtual machines to submit tests reports to the dashboard<br />
** Created Popup window when an error message appears in pre-processing and segmentation<br />
** EMSegmenter works now with different image data types (short, float,...)<br />
** Removed several bugs in mrml structure<br />
<br />
* 10/8/10<br />
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory<br />
** Fixed the leaks in the nightly tests<br />
* 10/1/10<br />
** Removed command line nodes from mrml scene after the command line is executed<br />
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine<br />
** Added label - in addition to the tree - to show the selected anatomical tree node<br />
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)<br />
** Working on parallel execution of multiple instances of the EMSegmentCommandLine<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=59554Projects:ARRA:SlicerEM2010-10-24T00:35:59Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 10/23/10<br />
** Bug fixes for Slicer 3.6.2 release<br />
* 10/15/10<br />
** Added function for automatically generating Template File <br />
** Added function for downloading task files from web<br />
** Added CMTK to extension module<br />
** One can assign now tcl file when creating a new task<br />
** Added class name to all tabs<br />
** Tested command line<br />
** Created virtual machines to submit tests reports to the dashboard<br />
** Created Popup window when an error message appears in pre-processing and segmentation<br />
** EMSegmenter works now with different image data types (short, float,...)<br />
** Removed several bugs in mrml structure<br />
<br />
* 10/8/10<br />
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory<br />
** Fixed the leaks in the nightly tests<br />
* 10/1/10<br />
** Removed command line nodes from mrml scene after the command line is executed<br />
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine<br />
** Added label - in addition to the tree - to show the selected anatomical tree node<br />
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)<br />
** Working on parallel execution of multiple instances of the EMSegmentCommandLine<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=59318Projects:ARRA:SlicerEM2010-10-16T02:56:41Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 10/15/10<br />
** Added function for automatically generating Template File <br />
** Added function for downloading task files from web<br />
** Added CMTK to extension module<br />
** One can assign now tcl file when creating a new task<br />
** Added class name to all tabs<br />
** Tested command line<br />
** Created virtual machines to submit tests reports to the dashboard<br />
** Created Popup window when an error message appears in pre-processing and segmentation<br />
** EMSegmenter works now with different image data types (short, float,...)<br />
** Removed several bugs in mrml structure<br />
<br />
* 10/8/10<br />
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory<br />
** Fixed the leaks in the nightly tests<br />
* 10/1/10<br />
** Removed command line nodes from mrml scene after the command line is executed<br />
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine<br />
** Added label - in addition to the tree - to show the selected anatomical tree node<br />
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)<br />
** Working on parallel execution of multiple instances of the EMSegmentCommandLine<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=59317Projects:ARRA:SlicerEM2010-10-16T02:56:17Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 10/15/10<br />
* Added function for automatically generating Template File <br />
* Added function for downloading task files from web<br />
* Added CMTK to extension module<br />
* One can assign now tcl file when creating a new task<br />
* Added class name to all tabs<br />
* Tested command line<br />
* Created virtual machines to submit tests reports to the dashboard<br />
* Created Popup window when an error message appears in pre-processing and segmentation<br />
* EMSegmenter works now with different image data types (short, float,...)<br />
* Removed several bugs in mrml structure<br />
<br />
* 10/8/10<br />
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory<br />
** Fixed the leaks in the nightly tests<br />
* 10/1/10<br />
** Removed command line nodes from mrml scene after the command line is executed<br />
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine<br />
** Added label - in addition to the tree - to show the selected anatomical tree node<br />
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)<br />
** Working on parallel execution of multiple instances of the EMSegmentCommandLine<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=58323Projects:ARRA:SlicerEM2010-09-25T11:10:25Z<p>Pohl: /* Key Personnel */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
20% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
<br />
* 9/24/10<br />
** Added check to make sure that the user cannot delete the root node<br />
** Added a warning to avoid ambiguous input channel names<br />
** Added check for emtpy 'Task Name'<br />
** Added a label to show the selected node during specifying the priors<br />
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter <br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery></div>Pohlhttps://www.na-mic.org/w/index.php?title=MICCAI_2010&diff=58188MICCAI 20102010-09-21T05:43:33Z<p>Pohl: /* Tutorial Agenda */</p>
<hr />
<div>[[Image:miccai2010logo.jpg |right|800px]]<br />
== From MICCAI Algorithms to Clinical Translational Tools: The NA-MIC Platform ==<br />
<br />
'''Outline:''' [http://www.miccai2010.org/ MICCAI] offers a window on the technological breakthroughs in medical image computing, computer assisted interventions and surgical robotics that will allow for revolutionary progress in clinical care. A critical step to maximize the long-term positive impact of MICCAI algorithms is to foster their deployment, validation and concrete use by the clinical research community for whom they were developed.<br />
The objective of the tutorial is to introduce the challenges inherent in delivering advanced medical imaging technologies (image processing, analysis and interventional capabilities) to end users for clinical translational research and to present solutions available in the National Alliance for Medical Image Computing (NA-MIC) open-source software toolkit. The day begins with an overview of the software components of the NA-MIC kit, followed by multiple example applications in current use for clinical research, with a final optional hands-on tutorial session that guides participants through the process of building, testing and deploying an exemplar algorithm using the NA-MIC open-source software toolkit.<br />
<br />
Through concrete examples drawn from the translational research efforts of NA-MIC, this tutorial provides insights on practical approaches for bridging the gap between the scientific advances made by the biomedical imaging community and their widespread use in the clinical research community. By the end of the day course participants will know how to use the NA-MIC kit to facilitate greater use of their own algorithms by clinical end users.<br />
<br />
== Organizers == <br />
*Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School<br />
*Guido Gerig, Ph.D., The Scientific Computing and Imaging Institute (SCI), University of Utah<br />
*Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School<br />
*Martin Styner, Ph.D., Neuro Image Research and Analysis Laboratory, University of North Carolina <br />
<br />
== Logistics ==<br />
<br />
The tutorial will be held on Monday September 20, 2010 '''from 8:30 am to 6:00 pm in room 402A on the L4 level''' at the China National Convention Center (CNCC), No.7 Tianchen East Road, Chaoyang District, Beijing, China.<br />
<br />
To register for the tutorial, please visit the [http://www.miccai2010.org/ MICCAI 2010 ] website.<br />
== Tutorial format ==<br />
<br />
The tutorial consists of lectures and an optional instructor-led hands-on session with the participants programming on their own laptop computers. A technical training staff will be providing one-to-one assistance as needed.<br />
<br />
== Tutorial Faculty ==<br />
*Ron Kikinis, M.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School<br />
*Sonia Pujol, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School<br />
*Noby Hata, Ph.D., Surgical Planning Laboratory, Brigham and Women’s Hospital, Harvard Medical School <br />
*Guido Gerig, Ph.D.,The Scientific Computing and Imaging Institute (SCI), University of Utah<br />
*Killian Pohl, Ph.D., Section for Biomedical Image Analysis, University of Pennsylvania <br />
*Dinggang Shen, Ph.D., Radiology and BRIC, University of North Carolina School of Medicine <br />
*Martin Styner, Ph.D., Neuro Image Research and Analysis Laboratory, University of North Carolina <br />
*Stephan Aylward, Ph.D., Kitware, Inc.<br />
*Xiaodong Tao, Ph.D., Visualization & Computer Vision, GE Research<br />
<br />
== Tutorial Agenda == <br />
*8:45 am - 9:00 am: Introduction and goals of the workshop (Sonia Pujol) <br />
*9:00 am - 9:15 am: [[media:Kikinis-NA-MIC-2010-09-20.ppt|Overview of the National Alliance for Medical Image Computing (NA-MIC)]] (Ron Kikinis)<br />
*9:15 am - 9:45 am: [[media:NAMIC_Programming_Environment_MICCAI2010_SoniaPujol.pdf | NA-MIC Programming Environment]] (Sonia Pujol)<br />
*9:45 am - 10:15 am: [http://www.na-mic.org/Wiki/images/1/15/NAMIC_Testing_MICCAI2010_XiaodongTao.pdf ‘Hardening’ your software with the NA-MIC kit, regression tests and dashboard ](Stephen Aylward/Xiaodong Tao) <br />
*10:15 am - 10:30 am: Morning Tea/Coffee Break<br />
*10:30 am - 11:00 am: [[media:BuildingBridgesBetweenSoftwarePlatforms_MICCAI2010_SoniaPujol.pdf | Building bridges between complementary medical image analysis platforms (e.g. Freesurfer, BRAINS2, HAMMER) ]](Sonia Pujol) <br />
*11:00 am - 11:30 am: [[media:Kikinis-How to work with NA-MIC-2010-09-20.ppt|How to participate in NA-MIC: collaboration grants, user and developer community (Kikinis)]]<br />
*11:30 am - 12:00 pm: Exemplar Clinical Research Applications: Image-Guided Therapy (Hata)<br />
*12:00 pm - 1:00 pm: Lunch <br />
*1:00 pm - 3:00 pm: Exemplar Clinical Research Applications <br />
**1:00 pm - 1:30 pm: Image Registration (Dinggang Shen) <br />
**1:30 pm - 2:00 pm: Image Segmentation: [[media:MICCAI10-Tutorial-Pohl.pdf | EM Segmenter]] (Kilian Pohl) and Automatic Brain Segmentation [[media:NAMIC-ABC-MICCAI2010b.pdf | ABC (Guido Gerig) ]]<br />
**2:00 pm - 2:30 pm: [[media:2010_09_CortThick-NAMIC-MICCAI.pdf | Cortical Thickness Measurements (Martin Styner) ]]<br />
**2:30 pm - 3:00 pm: Diffusion Tensor Imaging (Sonia Pujol, Guido Gerig [[media:DTI_NAMIC-MICCAI2010.pdf | Gerig-Slides]]) <br />
*3:00 pm - 3:30 pm: Afternoon Tea/Coffee Break<br />
*3:30 pm - 3:45 pm: [[media:Kikinis-Slicer Community-2010-09-20.ppt|Other examples from the community]] (Ron Kikinis)<br />
*3:45 pm - 5:30 pm: Optional Hands-on Session: [[media:ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf | Interfacing your MICCAI algorithm with the NA-MIC open-source toolkit: the ‘Hello Python’ tutorial ]](Sonia Pujol)<br />
*5:30 pm - 6:00 pm: Open Discussion and one-on-one consultations for individual projects<br />
<br />
== Preparation for the tutorial ==<br />
<br />
In preparation for the optional hands-on session, please install the [http://www.slicer.org/pages/Special:SlicerDownloads Slicer3.6 release version] appropriate to the platform you'll be using, and the [[media:HelloPython.zip | HelloPython dataset]] Hardware minimum requirement: 2GB of main memory and graphics hardware acceleration with 256 MB of dedicated graphics memory (nvidia preferred). <br />
<br />
[[media:MICCAI2010_T2tutorial_NAMIC_Draft_Tutorial_Notes.pdf| Draft Tutorial Notes]]<br />
<br />
[[media:MICCAI2010_T2tutorial_NAMIC_flyer.pdf| Tutorial flyer]]<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Pohlhttps://www.na-mic.org/w/index.php?title=File:MICCAI10-Tutorial-Pohl.pdf&diff=58187File:MICCAI10-Tutorial-Pohl.pdf2010-09-21T05:43:11Z<p>Pohl: uploaded a new version of "File:MICCAI10-Tutorial-Pohl.pdf"</p>
<hr />
<div></div>Pohlhttps://www.na-mic.org/w/index.php?title=Projects:ARRA:SlicerEM&diff=58122Projects:ARRA:SlicerEM2010-09-18T03:37:15Z<p>Pohl: /* Progress */</p>
<hr />
<div>[[Projects:ARRASuplements|Back to Slicer ARRA home page]]<br />
=Aim=<br />
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.<br />
<br />
=Research Plan=<br />
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence. <br />
<br />
The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.<br />
<br />
The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.<br />
<br />
The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.<br />
= Events =<br />
* Advanced EMSegmenter Training : How to parametrize the tool<br />
** Where: 1249 Bolyston Street, Boston, MA<br />
** When: 10 am - 1 pm , Feb 23, 2010<br />
<br />
=Key Personnel=<br />
10% Kilian Pohl <BR><br />
95% Dominique Belhachemi <BR><br />
5% Daniel Haehn<BR><br />
Kitware (Project Manager: Jean-Christophe Fillion-Robin)<br />
<br />
= Documentation =<br />
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6<br />
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]<br />
<br />
=Progress=<br />
* 9/17/10<br />
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)<br />
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build<br />
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step<br />
** 959 fixed: EMSegmenter ignores option --disableMultithreading<br />
** Added progress dialogs for pre-processing and segmentation<br />
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release <br />
* 9/10/10<br />
** Investigating a critical segfault bug 948+958<br />
** Reviewing use of the extension manager for our needs<br />
** Resolved bugs 970, 959, 944, 943<br />
* 9/3/10<br />
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)<br />
** Now possible to design step directly from QtDesigner<br />
** Discussed integration of PNL kMeans pipeline into Slicer 3.6<br />
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6<br />
** Discussed differences between the SBIA cluster and the BWH cluster,<br />
*** Conclusion: SGE seems to be easier to handle than Lava<br />
** Working on bug 959: EMSegmenter ignores option --disableMultithreading<br />
<br />
* 8/27/10<br />
** Integrated Workflow manager with QtModule<br />
** Review Workflow manager API<br />
** Fix bug related to PythonQt wrapping<br />
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree<br />
** Updated EMSegmenter related Wiki pages<br />
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)<br />
*** working on related bugs 954, 955, 948 <br />
*** changing some stderr output to stdout<br />
** Updating EMSegmenter tutorial for Slicer 3.6<br />
* 8/20/10<br />
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.<br />
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]<br />
* 8/13/10<br />
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted<br />
* 8/6/10 <br />
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt<br />
** Discuss how TCL script interacted with the KWWidgets workflow manager<br />
* 7/30/10<br />
** The port of the Workflow manager is initiated<br />
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow<br />
** Ability to script task in python is something important. Re-prioritize the task.<br />
** Discussed how dynamic panel could be ported.<br />
* 7/23/10 <br />
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]<br />
** Created initial directory structure<br />
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module<br />
** The port of existing TCL function related to processing is low priority<br />
* 7/16/10<br />
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon. <br />
* 7/9/10<br />
** Remove bugs <br />
** Set up contract with Kitware to port GUI to QT <br />
* 7/2/10<br />
** Hired Dominique Belhachemi<br />
** Transfered grant from IBM to UPenn<br />
** Wrote Progress Report <br />
* 6/25/10<br />
** Addressed all EMSegmenter bug in Mentis <br />
* 6/18/10<br />
** Revising task for MRI brain segmentation<br />
** Started search for new hire<br />
** Make EMSegmenter work with Slicer Superbuild<br />
* 6/11/10<br />
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface <br />
** Fixed major bugs so that Slicer 3 does not crash when creating a new task<br />
* 6/04/10<br />
** Imbedded BRAINSFit registration in the pipeline<br />
* 5/28/10<br />
** Changed Simple version of EMSegmenter to work with new preprocessing structure <br />
* 5/21/10<br />
** Fixed class overview window <br />
* 5/14/10<br />
** Fixed Intensity graph distribution display <br />
* 5/07/10<br />
** Fixed EMSegmenter command line module <br />
* 4/30/10<br />
** Debugged EMSegmenter for Slicer 3.6 release <br />
* 4/23/10<br />
** Added segmentation button at each Step of the Wizard<br />
** Integration of 3D/2D Bounding Box selection <br />
*4/16/10<br />
** Updated Slicer 3.6 Documentation<br />
** Modified workflow of Slicer 3.6<br />
*4/9/10<br />
** Created simple interface for preprocessing<br />
*4/2/10 <br />
** Incorporated Bug fixes from Slicer 3.4 into trunk <br />
** Removed bugs so that selecting tasks from a list properly works <br />
** Rolled EMSegmenter back to Slicer version 3.4<br />
** EMSegmenter Research environment now compiles under windows<br />
*3/26/10 Help users of EMSegment to adopt the tools to their needs <br />
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation <br />
*3/12/10 Start organizing tutorials for EMSegmenter<br />
*3/05/10 Extended first step in EMSegmenter to include default task list <br />
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation. <br />
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images<br />
*2/12/10 Presented Slicer to IBM Health Care Division <br />
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM <br />
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3 <br />
*1/22/10 Created slides for NAC Site visit<br />
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team<br />
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data <br />
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4<br />
*12/25/09 Setup Slicer environment for new hire <br />
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter<br />
*12/11/09 Learned about programming user interfaces in Qt <br />
*12/04/09 Interviewed applicant for Post Doc position to work on this project <br />
*11/29/09 Removed bugs related to updated CMake version<br />
*11/20/09 Organize bugs related to EMSegmenter <br />
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion<br />
** Sylvain will fix EMSEgmenter bugs Slicer 3.5<br />
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier<br />
** Andriy is developing a segmentation pipeline for the Wake Forest Data<br />
** Stuart will do testing of the EMSegmenter module<br />
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer<br />
*10/30/09 Organized Monthly TCon between EMSegmenter developers <br />
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3<br />
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR><br />
<br />
= Image gallery =<br />
<br />
<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt"><br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))<br />
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)<br />
</gallery></div>Pohl