NAMIC Wiki - User contributions [en]

Call for Identification of Medical Image Computing Grant Applications

2012-09-04T18:34:54Z

Aaron carass: /* Signed */ Added IACL.

[http://en.wikipedia.org/wiki/Medical_image_computing Medical Image Computing] (MIC) is a young field of research. To the best of our knowledge, there is no study section at NIH specializing on this topic. This is in contrast to the well established field of [http://en.wikipedia.org/wiki/Medical_imaging Medical Imaging], which is focused on improving image acquisition and reconstruction and has its own specialized study section.

We would like to raise the visibility of the field of Medical Image Computing (MIC) with the long term goal of initiating the creation of a study section focused on our field. This would provide a better match not only of the individual reviewers but also of the study section as a whole, which would be better attuned to MIC content. NIH needs evidence that enough grants on the topic are submitted at sufficient frequency to initiate this process. The typical threshold is around 20 submissions per cycle. Typically, an ad-hoc study section is created first, which can later be converted to a permanent study section if the stream of applications is sustained over several application cycles.

This is a call to the Medical Image Computing community. When submitting a MIC themed grant application to the NIH, please include the term '''Medical Image Computing''' in your grant summary and the keywords. You don't need to do anything else, just add the term. If, as a community, we can sustain the volume of applications that are labeled like this, then we can lobby for the process of study section formation to begin.

Our goal is to use the existing policies and governance to create a completely valid avenue for Medical Image Computing grant applications to compete against others in this field on equal footing and for the NIH reviewers to select the best science and engineering in this field with the highest potential to improve medical care. This will improve the reviewing system relative to the current state where Medical Image Computing applications are sent to a variety of different study sections and are evaluated by reviewers with core competences largely outside the MIC field.

=Actions Requested=
* Please include '''Medical Image Computing''' in the summary and keywords of all your future grant applications to NIH.
* Review the wikipedia page on [http://en.wikipedia.org/wiki/Medical_image_computing Medical Image Computing]. Improve the wikipedia page by editing and adding content.

=Signed=
#[http://people.csail.mit.edu/polina Polina Golland]
#[http://www.spl.harvard.edu/pages/People/kikinis Ron Kikinis]
#[http://www.martinstyner.org Martin Styner]
#[http://www.sci.utah.edu/people/gerig.html Guido Gerig]
#[http://www.na-mic.org/Wiki/index.php/Algorithm:BU Allen Tannenbaum]
#[http://lmi.bwh.harvard.edu/~westin Carl-Fredrik Westin]
#[http://www.cs.utah.edu/~crj/ Chris Johnson]
#[http://www.stanford.edu/people/Sandy.Napel Sandy Napel]
#[http://www.cs.queensu.ca/~gabor Gabor Fichtinger]
#[http://www.iacl.ece.jhu.edu/ Aaron Carass]

2010 Summer Project Week SPECTRE

2010-06-17T14:51:21Z

Aaron carass: Expanded the objectives.

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* BWH: Nicole Aucoin
* JHU: Min Chen

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

Further integration of the Java SPECTRE skull stripping module into Slicer3.

Specific potential enhancements include:
*CMake module integration using Ant to build SPECTRE.
*Fixing/replacing the outdated tck wrappers with Python wrappers.
*Core components of SPECTRE currently act independently, could be homogenized.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach is to integrate SPECTRE as an extension.
The main challenge to this approach is setting up a web site with a stable jar file and tcl wrapper.

Our plan for the project week is to first try out a temporary location for the jar file and tcl wrapper and then come up with a plan for updates.

SPECTRE outputs will be modified to be compatible with Slicer image types(i.e. intensity, mask, etc.)

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

Tcl wrapped Java jar files have been integrated into Slicer3 already, so hopefully no major infrastructure changes will be required.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a:
#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==

</div>

NA-MIC JHU Skull Stripping Collaboration

2010-05-24T20:26:06Z

Aaron carass: /* Publications */ Added 'Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities'.

__NOTOC__
Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]

[[Image:JHUSkullStripping.png|300px]]

==Grant#==
R21EB009900
== Key Personel==
* JHU: Jerry L. Prince, PI, Aaron Carass, Min Chen, Snehashis Roy
* NA-MIC: Nicole Aucoin, Ron Kikinis

==Funding Duration==
08/01/2009-07/31/2011
==Goals of the Project==
The primary goals of this proposal are to enhance the NA-MIC code base with a segmentation algorithm that is capable of skull stripping and segmenting both cerebrum and cerebellum separately or collectively in a way which provides accuracy comparable to human raters.
==Aims==
#Rewrite SPECTRE using the NA-MIC software methodology for inclusion in Slicer 3D
#Complete the algorithms necessary for isolating and establishing a coordinate system on the cerebellum
#Parameters will be optimized in order for SPECTRE to perform well with a variety of differelty aquired data
#Compare SPECTRE against all publically available (source or binary) skull-stripping software
==Current progress==
==References==
[[2009_Summer_Project_Week_Skull_Stripping | Summer 2009 Project Week]]
==Publications==
* A. Carass, M.B. Wheeler, J. Cuzzocreo, P.-L. Bazin, S.S. Bassett and J.L. Prince, '''"A Joint Registration and Segmentation Approach to Skull Stripping"'''. Proceedings of the Fourth IEEE International Symposium on Biomedical Imaging (ISBI 2007), Arlington, VA, April 12-15, 2007.
* K. Covington, E. McCreedy, M. Chen, A. Carass, N. Aucoin, and B.A. Landman, '''"Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities"'''. Annual ORNL Biomedical Science and Engineering Conference (BSEC 2010), Oak Ridge, Tennessee, May 25-26, 2010.

NA-MIC JHU Skull Stripping Collaboration

2010-05-24T20:12:35Z

Aaron carass: /* Key Personel */ Update.

__NOTOC__
Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]

[[Image:JHUSkullStripping.png|300px]]

==Grant#==
R21EB009900
== Key Personel==
* JHU: Jerry L. Prince, PI, Aaron Carass, Min Chen, Snehashis Roy
* NA-MIC: Nicole Aucoin, Ron Kikinis

==Funding Duration==
08/01/2009-07/31/2011
==Goals of the Project==
The primary goals of this proposal are to enhance the NA-MIC code base with a segmentation algorithm that is capable of skull stripping and segmenting both cerebrum and cerebellum separately or collectively in a way which provides accuracy comparable to human raters.
==Aims==
#Rewrite SPECTRE using the NA-MIC software methodology for inclusion in Slicer 3D
#Complete the algorithms necessary for isolating and establishing a coordinate system on the cerebellum
#Parameters will be optimized in order for SPECTRE to perform well with a variety of differelty aquired data
#Compare SPECTRE against all publically available (source or binary) skull-stripping software
==Current progress==
==References==
[[2009_Summer_Project_Week_Skull_Stripping | Summer 2009 Project Week]]
==Publications==
* Aaron Carass, M. Bryan Wheeler, Jennifer Cuzzocreo, Pierre-Louis Bazin, Susan S. Bassett and Jerry L. Prince, A Joint Registration and Segmentation Approach to Skull Stripping. Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2007.

2010 Winter Project Week SPECTRE 3DSlicer Integration

2010-01-06T19:14:14Z

Aaron carass: /* Presentations */ Moved link around.

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
<! --Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.-- >
</gallery>

==Key Investigators==
* BWH: Nicole Aucoin
* JHU: Aaron Carass, Min Chen
* GE: Jim Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

Integration of SPECTRE Skull Stripping software into the NAMIC Toolkit via the Slicer3 CLI framework.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach: integration of software which will segment and provide coordinate reference frames for the Cerebrum (akin to the Talairach space), the Cerebellum (see reference below for K. Rehm), and for the Brainstem.

This will be achieved through integration of the Java Imaging Software Toolkit (JIST) into the Slicer3 framework and then testing and evaluation of JIST components for completing the necessary components to provide this system.

The main challenge is supporting Java command line executables in 3D Slicer.

Our plan is first to facilitate Java command line module discovery and execution, by adding support for the --xml argument to SPECTRE, and adding support for tcl wrapping scripts in 3DSlicer.
Then integrate SPECTRE into the NAMIC toolkit by crafing a CMakeLists.txt file to allow it to be built easily.
Create a NITRC project and a 3D Slicer extension that can be either downloaded or built on any platform.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

A proof of concept sample Java HelloWorld application has been added to 3D Slicer.

</div>
</div>

==Presentations==
[[Media:2010-NA-MIC-Prince.ppt|Powerpoint]] presentation given by Jerry L. Prince on the status of the integration of SPECTRE as a module within Slicer, given at the 2010 Winter AHM in Utah.

<div style="width: 97%; float: left;">

==References==
*K. Rehm's 2000 HBM abstract, 'Use of Cerebellar Landmarks To Define a Coordinate System and an Isolation Strategy'
</div>

2010 Winter Project Week SPECTRE 3DSlicer Integration

2010-01-06T18:57:12Z

Aaron carass: Added link to File:2010-NA-MIC-Prince.ppt.

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
<! --Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.-- >
</gallery>

==Key Investigators==
* BWH: Nicole Aucoin
* JHU: Aaron Carass, Min Chen
* GE: Jim Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

Integration of SPECTRE Skull Stripping software into the NAMIC Toolkit via the Slicer3 CLI framework.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach: integration of software which will segment and provide coordinate reference frames for the Cerebrum (akin to the Talairach space), the Cerebellum (see reference below for K. Rehm), and for the Brainstem.

This will be achieved through integration of the Java Imaging Software Toolkit (JIST) into the Slicer3 framework and then testing and evaluation of JIST components for completing the necessary components to provide this system.

The main challenge is supporting Java command line executables in 3D Slicer.

Our plan is first to facilitate Java command line module discovery and execution, by adding support for the --xml argument to SPECTRE, and adding support for tcl wrapping scripts in 3DSlicer.
Then integrate SPECTRE into the NAMIC toolkit by crafing a CMakeLists.txt file to allow it to be built easily.
Create a NITRC project and a 3D Slicer extension that can be either downloaded or built on any platform.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

A proof of concept sample Java HelloWorld application has been added to 3D Slicer.

</div>
</div>

==Presentations==
Powerpoint presentation given by Jerry L. Prince on the status of the integration of SPECTRE as a module within Slicer, given at the 2010 Winter AHM in Utah. [[File:2010-NA-MIC-Prince.ppt]]

<div style="width: 97%; float: left;">

==References==
*K. Rehm's 2000 HBM abstract, 'Use of Cerebellar Landmarks To Define a Coordinate System and an Isolation Strategy'
</div>

File:2010-NA-MIC-Prince.ppt

2010-01-06T18:49:34Z

Aaron carass: Powerpoint presentation given by Jerry L. Prince on the status of the integration of SPECTRE as a module within Slicer.

Powerpoint presentation given by Jerry L. Prince on the status of the integration of SPECTRE as a module within Slicer.

Main Page

2008-07-03T20:26:22Z

Aaron carass: Fooling around.

__NOTOC__
== '''Welcome to the NA-MIC Wiki!''' ==
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"| [[Image:NIH_Logo.png|[[Image:NIH_Logo.png|Image:NIH_Logo.png]]]][[Image:Dhhs_logo.png|[[Image:Dhhs_logo.png|Image:Dhhs_logo.png]]]]

''Welcome!''

These wiki pages are meant to encourage quick and efficient communication among the participating investigators and the interested users of NA-MIC. If you are interested in the BIG picture or need an introduction to our project please go to our main web page [http://www.na-mic.org/ NA-MIC]. To get an idea of the ongoing activities in this project, follow the links in the Navigation box on the left side of this page: Cores and Projects contains information about the activities in the individual NA-MIC cores as well as cross-NCBC activities, the Events pages contains information about upcoming and past NA-MIC events including teleconferences, and the Resources pages contain information about NA-MIC software.
| style="background: #ebeced" colspan="2" align="center"| <b>Featured Paper</b>
|-
| style="background: #ebeced"|[[Image:Shape-analysisdspaceid1294.jpg|center|250px|Shape Analysis Workflow]]
| style="background: #ebeced"|Workflow for processing segmentations to perform shape based group comparisons. <br>
For more information click [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1294 '''here'''].
|}
<br>
----
'''<big> [[Events|Events]] </big>'''

A list of all our past and upcoming events.

'''<big> [[NA-MIC_Collaborations|NA-MIC Collaborations]] </big>'''

This is a list of our internal and external collaborative projects.

'''<big> [[NA-MIC-Kit|NA-MIC Kit]] </big>'''

The NA-MIC Kit consists of software and software engineering methods that are used and developed by NA-MIC, including [[Slicer3|Slicer3]].

'''<big> [[Engineering:Programming_Events|NA-MIC Programming/Project Events]] </big>'''

NA-MIC Project Week is a hands on activity -- programming using the NA-MIC Kit, algorithm design, and clinical applications. The link above leads to results from project weeks held since 2005.
<br>
----

= Pages for Affiliated Research Teams and Organizations =

''' [[NIH-Page|NIH Page]] '''

* This page contains useful information provided by our NIH officers.

''' [[Historic-Links|Other Links]] '''