2008 Winter Project Week Tractography Meeting Notes - Revision history

Grundlett: Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

2017-07-10T18:22:33Z

Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/"

RandyGollub at 23:54, 15 January 2008

2008-01-15T23:54:33Z

RandyGollub at 23:51, 15 January 2008

2008-01-15T23:51:02Z

RandyGollub at 06:03, 15 January 2008

2008-01-15T06:03:28Z

RandyGollub at 09:12, 14 January 2008

2008-01-14T09:12:34Z

RandyGollub: /* Notes */

2008-01-14T08:38:23Z

Notes

RandyGollub at 08:34, 14 January 2008

2008-01-14T08:34:19Z

RandyGollub at 08:32, 14 January 2008

2008-01-14T08:32:11Z

RandyGollub at 08:31, 14 January 2008

2008-01-14T08:31:11Z

RandyGollub at 08:29, 14 January 2008

2008-01-14T08:29:54Z

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 # The new mBIRN compliant DTI data from MIND used for the tractography comparison used the following preprocessing steps: a) Registration (FLIRT for DTI to structural MR), b)EPI distortion correction (we used FUGUE), ITK?
-It will be a priority to develop these preprocessing functions within Slicer-3: Registration became available this Jan. 2008: See update by Stephen Aylward in AHM Registration breakout session: Slides: [http://www.na-mic.org/Wiki/images/f/f2/2008-01-AHM-Aylward-RegistrationClasses.ppt] / Eddy-current and EPI correction see plan by Westin/Fletcher/Whitaker above.
+It will be a priority to develop these preprocessing functions within Slicer-3: Registration became available this Jan. 2008: See update by Stephen Aylward in AHM Registration breakout session: Slides: [https://na-mic.org/w/images/f/f2/2008-01-AHM-Aylward-RegistrationClasses.ppt] / Eddy-current and EPI correction see plan by Westin/Fletcher/Whitaker above.
 The DTI workshop group concluded that the list provided by Alex matched deliverables proposed by developers very well.

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 # ROIs still need work
 # Metrics for comparison still need work
 # Randy Gollub met w/ Dan Marcus re: data management needs of this project. Dan Marcus set up a mirror of our data repository on Central XNAT (http://central.xnat.org/, however, we will need to continue to use SRB to share image and analysis files for the next several months.

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 == Brief Summary ==
 '''"We know when the track is bad (or ugly) but we don't know when it is good." CF Westin'''
-# All sites could analyze data
+# All sites could analyze new dataset
-# All sites could generate all requested tracks
+# All sites could generate all requested tracks (Ugly R fornix), missing arcuate fasiculus
-# ROIs need work
+# ROIs still need work
-# Ugly R fornix
+# Metrics for comparison still need work
-# Dan Marcus set up a mirror of our data repository on Central XNAT (http://central.xnat.org/)
+# Randy Gollub met w/ Dan Marcus re: data management needs of this project. Dan Marcus set up a mirror of our data repository on Central XNAT (http://central.xnat.org/, however, we will need to continue to use SRB to share image and analysis files for the next several months.
 == Action Plans ==
 * Read this whole page and then edit to make additions and/or corrections (Guido, CF and Randy did their best to capture the contents and plans)
 * Upload your presentation slides to the Workshop page (http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_Tractography)
-* Upload to our SRB workspace the DTI registered (using FSL's FLIRT) Freesurfer generated white matter mask in nrrd format at same resolution as DTI data for each subject (Anastasia, Sylvain, bug-reporter as needed).
+* We will use the structure of regular bi-weekly T-cons, Tuesdays at 11 AM EST/ 9 AM MST/ 8 AM PST to continue to move this project forward.
 * Upload to our SRB workspace DTI registered additional neuroanatomical label maps for tracks (e.g. ending structures) adding arcuate fasiculus as agreed upon by clinical break-out group at 3-4 PM (Randy/Marek/Sonia).
 * Upload to our SRB workspace helical phantom binary code and other materials with documentation (Nathan Hageman) and download to play with (all others)
 <br>
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 Core-2 teams will visit Core-1 developers for face-to-face discussion of transfer and integration of tools. It was decided in a separate meeting that first, the Utah groups will host the engineering Core-2 people for discussing Slicer-3 integration, including DTI module transfer.
-==Notes==
+==Miscellaneous Meeting Notes==
 From Casey's presentation:  Made suggestion of using one set of ROI specifications for an entire study in atlas space, mapping them back to the individual subjects.
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-Sonia's preliminary cross-algorithm study:
+From Sonia's preliminary cross-algorithm study:
 #rank order of qualitative accuracy (strongly underscores need to clarify the clinical goal of the tractography results)

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 # ROIs need work
 # Ugly R fornix
 == Action Plans ==
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 * Upload to our SRB workspace helical phantom binary code and other materials with documentation (Nathan Hageman) and download to play with (all others)
 * Regular bi-weekly T-cons, Tuesdays at 11 AM EST/ 9 AM MST/ 8 AM PST
-* First T-con will be Tuesday January 22
+* First T-con will be Tuesday January 22, reminder with call in number to be sent out shortly.
 * Agenda for first T-con will be review of Nathan Hageman's helical phantom and choice of metrics for all to generate and share.
 * All sites analyze full n = 9 test/retest data set and sent agreed upon metrics to Sonia in time for Summer Programmer's week.
 * Intermediate goals to be set by group in our regular T-cons
 <br>

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 == Action Plans ==
 * Upload your presentation slides to the Workshop page (http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_Tractography)
 * Upload to our SRB workspace the DTI registered (using FSL's FLIRT) Freesurfer generated white matter mask in nrrd format at same resolution as DTI data for each subject (Anastasia, Sylvain, bug-reporter as needed).

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 ==Notes==
-From Casey's presentation:  Could do tractography for all tracks.  Made suggestion to .  His Atlas presentation brought up idea of using one set of ROI specifications for an entire study in atlas space and map them back to the individual.
+From Casey's presentation:  Made suggestion of using one set of ROI specifications for an entire study in atlas space, mapping them back to the individual subjects.
 From John's presentation: His method required that he had to shrink the provided ROIs for uncinate fasciulus and corpus callosum to  make his method work.  Then could generate fiber volumes for each tract.  His tracts all STOP at ROIs (end points).  If given ROIs farther apart could generate longer tracts.  Needed a white matter mask- created his own with Tri by thresholding FA (>0.15). Discussion regarding whether the ROIs based on Susumu Mori's criteria would actually be optimal or even work for every method.
-From Tri's presentation: Able to generate all tracks with given ROIs.  Needed white matter mask (see above).  30 minutes/tract on 63GB computer.  Seed with source, filter with sink.  Had to cut uncinate fasciulus.  For later statistical analysis, considered only non-zero connectivity value voxels.  Reminds us that bundle thickness is related to both uncertainty and physical radius
+From Tri's presentation: Able to generate all tracks with given ROIs.  Needed white matter mask (see above).  30 minutes/tract on 63GB computer.  Seed with source, filter with sink.  Had to cut uncinate fasciulus.  For later statistical analysis, considered only non-zero connectivity value voxels.  Reminds us that bundle thickness is related to both uncertainty and physical radius.
+From Vince Magnotta's presentation: GTRACT works well for forceps major and minor, internal capusule.  A Fast Marching algorithm is better for fornix, hippocampus-cingulum and cingulum.  For the Fast Marching algorithm, modified the algorithm to use cost image generations based on tensor and anisotropy, gradient descent. His algorithm would perform "better" for core of cingulum bundle, needs a smaller, more focal ROI.  For uncinate, couldn't get it to bend around, would need intermediate ROIs.
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-From Carlo:
+Comments from Carlo:
-#Commended us for making effort against this tough problem and for the decision  to control pre-processing steps
+#Commended us for making effort against this tough problem and for the decision to control pre-processing steps
 #What is the impact of adjusting parameters within an algorithm on the outcome metrics?  May need to explore this in addition to the cross algorithm assessments.
 #What is the effect of the tissue properties that surround the track on results within and across algorithm.

← Older revision		Revision as of 08:34, 14 January 2008
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	== How to approach Test- Retest data ==		== How to approach Test- Retest data ==
−	~~Start~~ discussion	+	Never even started discussion of this topic!