NAMIC Wiki - User contributions [en]

Call for Identification of Medical Image Computing Grant Applications

2012-09-04T18:42:55Z

Bennett: /* Signed */

[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]
#[https://masi.vuse.vanderbilt.edu/index.php/Main_Page Bennett Landman]

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-25T16:40:00Z

Bennett:

__NOTOC__
<gallery>

Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
<ul>
<li>Surveyed existing CLI interface and identified areas for extension
<li>Explored integration of external modules into the s3ext extension framework
<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
<li>Communicated with XIP team about generating a common/compatible interface layer
</ul>
''See detailed results below.''

</div>
</div>

<div style="width: 970%; float: left;">

==Results==
'''Areas for Investigation with CLI and Existing Limitations'''
<ul>
<li>Multiple “programs” per executable.
<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
<li>Report to both stdout (via xml markup) [optional]
<li>Generalize the calling syntax --- especially the ability to control argument structure.
<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
<li>Provide preferred and supported format syntax for resource (file) based communication.
<li>Ability to model dependencies between flags
<li>Workflow level perspective – “sample a bunch of points” = harness level things
<li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
</ul>

'''Slicer 3 Extension System'''
<ul>
<li>Recognized the need for a interface specific compatability checks (rather than build level checks) because external modules might not be built on the build farm.
<li>Emphasized that module availability might vary by platform. Some modules could be win-only/redhat only/ubuntu only/linux kernel X.Y only/etc.
<li>Suggested the use of a Ubuntu "multi-verse" system for accessing/discovering external modules
<li>Recognized that external modules may be very large and require size checks/download monitor/cancel/resume/etc.
<li>Suggested that EULA's would be required for modules. Users would need to agree to these licenses prior to download (e.g., difference between external multi-verse and Slicer-licensed modules on the build farm).
</ul>

'''JIST/MIPAV->CLI Bridge'''
<ul>
<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
<li>

<div style="width:400px; margin:0 auto;><pre>
Adding Noise edu.jhu.bme.smile.demo.AddingNoise
Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting
Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra
Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic
Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVol
Demo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo
staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo
...
</pre></div>

<li> Automated self-documenting executables
<li>
<div style="width:99.5%; margin:0 auto;>
<pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
[-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
<arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
[-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
[-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
[-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
[-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
[-outExecution] [-outRegistered] [-outTransformation]
[-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
<arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
-h,--help Print this message.
-inApply <arg> Apply rotation [option:All|X|Y|Z] (required,
default=All)
-inCoarse <arg> Coarse angle increment [double] (required,
default=15.0)
-inCost <arg> Cost function [option:Correlation ratio|Least
squares|Normalized cross correlation|Normalized
mutual information] (required,
default=Correlation ratio)
-inDegrees <arg> Degrees of freedom [option:Rigid - 6|Global
rescale - 7|Specific rescale - 9|Affine - 12]
(required, default=Affine - 12)
-inFine <arg> Fine angle increment [double] (required,
default=6.0)
-inInput <arg> Input Weighted volume [file] (optional)
-inMaximum <arg> Maximum angle [double] (required, default=30.0)
-inMinimum <arg> Minimum angle [double] (required, default=-30.0)
-inMultiple <arg> Multiple of tolerance to bracket the minimum
[integer] (required, default=10)
-inNumber <arg> Number of iterations [integer] (required,
default=2)
-inNumber2 <arg> Number of minima from Level 8 to test at Level 4
[integer] (required, default=3)
-inOutput <arg> Output interpolation [option:Trilinear|Bspline
3rd order|Bspline 4th order|Cubic
Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc|Nearest Neighbor]
(required, default=Trilinear)
-inReference <arg> Reference Weighted volume [file] (optional)
-inRegistration <arg> Registration interpolation
[option:Trilinear|Bspline 3rd order|Bspline 4th
order|Cubic Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc] (required,
default=Trilinear)
-inSkip <arg> Skip multilevel search (Assume images are close
to alignment) [boolean] (required, default=false)
-inSource <arg> Source Volumes [file collection: semi-colon
delimited list] (required, default=)
-inSubsample <arg> Subsample image for speed [boolean] (required,
default=true)
-inTarget <arg> Target volume [file] (required)
-inUse <arg> Use the max of the min resolutions of the two
datasets when resampling [boolean] (required,
default=true)
-outExecution Execution Time [string] (required)
-outRegistered Registered Volumes [file collection: semi-colon
delimited list] (required, default=)
-outTransformation Transformation Matrix [matrix semi-colon
delimited rows in text] (optional)
-outTransformation2 Transformation Matrices [file] (optional)
-outTransformations Transformations [file collection: semi-colon
delimited list] (required, default=)
-xDir <arg> Request Output: Processing Directory (default
current) [directory] (optional)
-xFile <arg> Request Output: Results File (default output.txt)
[file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/
</pre></div>
<li> These features will be released in the next version of JIST.
</ul>

'''Framework for Interoperability of Neuroimaging Software'''
<ul>
<li>Existing Slicer CLI can be bridge to ''almost'' any command line system through use of shell scripts.
<li>These scripts are platform specific and are complex to extend for larger projects --- do we write script factories? Factories for platform specific factories?
<li>If we are going to address the problem of inter-communication, perhaps it would be best to develop a SIMPLE architecture agnostic XML syntax for functionality query, programmatic direction, and result response.
<li>Started a NITRC project (FOPA - Framework for Open Programmatic Access) to develop multi-platform reference implementations. http://www.nitrc.org/projects/fopa/
</ul>
==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-25T16:09:14Z

Bennett:

__NOTOC__
<gallery>

Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
<ul>
<li>Surveyed existing CLI interface and identified areas for extension
<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
<li>Communicated with XIP team about generating a common/compatible interface layer
</ul>
''See detailed results below.''

</div>
</div>

<div style="width: 970%; float: left;">

==Results==
'''Areas for Investigation with CLI and Existing Limitations'''
<ul>
<li>Multiple “programs” per executable.
<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
<li>Report to both stdout (via xml markup) [optional]
<li>Generalize the calling syntax --- especially the ability to control argument structure.
<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
<li>Provide preferred and supported format syntax for resource (file) based communication.
<li>Ability to model dependencies between flags
<li>Workflow level perspective – “sample a bunch of points” = harness level things
<li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
</ul>

'''JIST/MIPAV->CLI Bridge'''
<ul>
<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
<li>

<div style="width:400px; margin:0 auto;><pre>
Adding Noise edu.jhu.bme.smile.demo.AddingNoise
Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting
Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra
Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic
Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVol
Demo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo
staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo
...
</pre></div>

<li> Automated self-documenting executables
<li>
<div style="width:99.5%; margin:0 auto;>
<pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
[-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
<arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
[-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
[-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
[-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
[-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
[-outExecution] [-outRegistered] [-outTransformation]
[-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
<arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
-h,--help Print this message.
-inApply <arg> Apply rotation [option:All|X|Y|Z] (required,
default=All)
-inCoarse <arg> Coarse angle increment [double] (required,
default=15.0)
-inCost <arg> Cost function [option:Correlation ratio|Least
squares|Normalized cross correlation|Normalized
mutual information] (required,
default=Correlation ratio)
-inDegrees <arg> Degrees of freedom [option:Rigid - 6|Global
rescale - 7|Specific rescale - 9|Affine - 12]
(required, default=Affine - 12)
-inFine <arg> Fine angle increment [double] (required,
default=6.0)
-inInput <arg> Input Weighted volume [file] (optional)
-inMaximum <arg> Maximum angle [double] (required, default=30.0)
-inMinimum <arg> Minimum angle [double] (required, default=-30.0)
-inMultiple <arg> Multiple of tolerance to bracket the minimum
[integer] (required, default=10)
-inNumber <arg> Number of iterations [integer] (required,
default=2)
-inNumber2 <arg> Number of minima from Level 8 to test at Level 4
[integer] (required, default=3)
-inOutput <arg> Output interpolation [option:Trilinear|Bspline
3rd order|Bspline 4th order|Cubic
Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc|Nearest Neighbor]
(required, default=Trilinear)
-inReference <arg> Reference Weighted volume [file] (optional)
-inRegistration <arg> Registration interpolation
[option:Trilinear|Bspline 3rd order|Bspline 4th
order|Cubic Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc] (required,
default=Trilinear)
-inSkip <arg> Skip multilevel search (Assume images are close
to alignment) [boolean] (required, default=false)
-inSource <arg> Source Volumes [file collection: semi-colon
delimited list] (required, default=)
-inSubsample <arg> Subsample image for speed [boolean] (required,
default=true)
-inTarget <arg> Target volume [file] (required)
-inUse <arg> Use the max of the min resolutions of the two
datasets when resampling [boolean] (required,
default=true)
-outExecution Execution Time [string] (required)
-outRegistered Registered Volumes [file collection: semi-colon
delimited list] (required, default=)
-outTransformation Transformation Matrix [matrix semi-colon
delimited rows in text] (optional)
-outTransformation2 Transformation Matrices [file] (optional)
-outTransformations Transformations [file collection: semi-colon
delimited list] (required, default=)
-xDir <arg> Request Output: Processing Directory (default
current) [directory] (optional)
-xFile <arg> Request Output: Results File (default output.txt)
[file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/
</pre></div>
<li> These features will be released in the next version of JIST.
</ul>

'''Framework for Interoperability of Neuroimaging Software'''
<ul>
<li>Existing Slicer CLI can be bridge to ''almost'' any command line system through use of shell scripts.
<li>These scripts are platform specific and are complex to extend for larger projects --- do we write script factories? Factories for platform specific factories?
<li>If we are going to address the problem of inter-communication, perhaps it would be best to develop a SIMPLE architecture agnostic XML syntax for functionality query, programmatic direction, and result response.
<li>Started a NITRC project (FOPA - Framework for Open Programmatic Access) to develop multi-platform reference implementations. http://www.nitrc.org/projects/fopa/
</ul>
==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-25T15:59:29Z

Bennett:

__NOTOC__
<gallery>

Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
<ul>
<li>Surveyed existing CLI interface and identified areas for extension
<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
<li>Communicated with XIP team about generating a common/compatible interface layer
</ul>
''See detailed results below.''

</div>
</div>

<div style="width: 970%; float: left;">

==Results==
'''Areas for Investigation with CLI and Existing Limitations'''
<ul>
<li>Multiple “programs” per executable.
<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
<li>Report to both stdout (via xml markup) [optional]
<li>Generalize the calling syntax --- especially the ability to control argument structure.
<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
<li>Provide preferred and supported format syntax for resource (file) based communication.
<li>Ability to model dependencies between flags
<li>Workflow level perspective – “sample a bunch of points” = harness level things
<li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
</ul>

'''JIST/MIPAV->CLI Bridge'''
<ul>
<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
<li><pre>
Adding Noise edu.jhu.bme.smile.demo.AddingNoise
Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting
Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra
Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic
Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVol
Demo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo
staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo
...
</pre>

<li> Automated self-documenting executables
<li><pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
[-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
<arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
[-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
[-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
[-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
[-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
[-outExecution] [-outRegistered] [-outTransformation]
[-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
<arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
-h,--help Print this message.
-inApply <arg> Apply rotation [option:All|X|Y|Z] (required,
default=All)
-inCoarse <arg> Coarse angle increment [double] (required,
default=15.0)
-inCost <arg> Cost function [option:Correlation ratio|Least
squares|Normalized cross correlation|Normalized
mutual information] (required,
default=Correlation ratio)
-inDegrees <arg> Degrees of freedom [option:Rigid - 6|Global
rescale - 7|Specific rescale - 9|Affine - 12]
(required, default=Affine - 12)
-inFine <arg> Fine angle increment [double] (required,
default=6.0)
-inInput <arg> Input Weighted volume [file] (optional)
-inMaximum <arg> Maximum angle [double] (required, default=30.0)
-inMinimum <arg> Minimum angle [double] (required, default=-30.0)
-inMultiple <arg> Multiple of tolerance to bracket the minimum
[integer] (required, default=10)
-inNumber <arg> Number of iterations [integer] (required,
default=2)
-inNumber2 <arg> Number of minima from Level 8 to test at Level 4
[integer] (required, default=3)
-inOutput <arg> Output interpolation [option:Trilinear|Bspline
3rd order|Bspline 4th order|Cubic
Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc|Nearest Neighbor]
(required, default=Trilinear)
-inReference <arg> Reference Weighted volume [file] (optional)
-inRegistration <arg> Registration interpolation
[option:Trilinear|Bspline 3rd order|Bspline 4th
order|Cubic Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc] (required,
default=Trilinear)
-inSkip <arg> Skip multilevel search (Assume images are close
to alignment) [boolean] (required, default=false)
-inSource <arg> Source Volumes [file collection: semi-colon
delimited list] (required, default=)
-inSubsample <arg> Subsample image for speed [boolean] (required,
default=true)
-inTarget <arg> Target volume [file] (required)
-inUse <arg> Use the max of the min resolutions of the two
datasets when resampling [boolean] (required,
default=true)
-outExecution Execution Time [string] (required)
-outRegistered Registered Volumes [file collection: semi-colon
delimited list] (required, default=)
-outTransformation Transformation Matrix [matrix semi-colon
delimited rows in text] (optional)
-outTransformation2 Transformation Matrices [file] (optional)
-outTransformations Transformations [file collection: semi-colon
delimited list] (required, default=)
-xDir <arg> Request Output: Processing Directory (default
current) [directory] (optional)
-xFile <arg> Request Output: Results File (default output.txt)
[file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/
</pre>
<li> These features will be released in the next version of JIST.
</ul>

'''Framework for Interoperability of Neuroimaging Software'''
<ul>
<li>Existing Slicer CLI can be bridge to ''almost'' any command line system through use of shell scripts.
<li>These scripts are platform specific and are complex to extend for larger projects --- do we write script factories? Factories for platform specific factories?
<li>If we are going to address the problem of inter-communication, perhaps it would be best to develop a SIMPLE architecture agnostic XML syntax for functionality query, programmatic direction, and result response.
<li>Started a NITRC project (FOPA - Framework for Open Programmatic Access) to develop multi-platform reference implementations. http://www.nitrc.org/projects/fopa/
</ul>
==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-25T15:59:07Z

Bennett:

__NOTOC__
<gallery>

Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
<ul>
<li>Surveyed existing CLI interface and identified areas for extension
<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
<li>Communicated with XIP team about generating a common/compatible interface layer
</ul>
''See detailed results below.''

</div>
</div>

<div style="width: 970%; float: left;">

==Results==
'''Areas for Investigation with CLI and Existing Limitations'''
<ul>
<li>Multiple “programs” per executable.
<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
<li>Report to both stdout (via xml markup) [optional]
<li>Generalize the calling syntax --- especially the ability to control argument structure.
<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
<li>Provide preferred and supported format syntax for resource (file) based communication.
<li>Ability to model dependencies between flags
<li>Workflow level perspective – “sample a bunch of points” = harness level things
<li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
</ul>

'''JIST/MIPAV->CLI Bridge'''
<ul>
<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
<li><pre width=100>
Adding Noise edu.jhu.bme.smile.demo.AddingNoise
Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting
Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra
Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic
Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVol
Demo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo
staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo
...
</pre>

<li> Automated self-documenting executables
<li><pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
[-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
<arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
[-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
[-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
[-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
[-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
[-outExecution] [-outRegistered] [-outTransformation]
[-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
<arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
-h,--help Print this message.
-inApply <arg> Apply rotation [option:All|X|Y|Z] (required,
default=All)
-inCoarse <arg> Coarse angle increment [double] (required,
default=15.0)
-inCost <arg> Cost function [option:Correlation ratio|Least
squares|Normalized cross correlation|Normalized
mutual information] (required,
default=Correlation ratio)
-inDegrees <arg> Degrees of freedom [option:Rigid - 6|Global
rescale - 7|Specific rescale - 9|Affine - 12]
(required, default=Affine - 12)
-inFine <arg> Fine angle increment [double] (required,
default=6.0)
-inInput <arg> Input Weighted volume [file] (optional)
-inMaximum <arg> Maximum angle [double] (required, default=30.0)
-inMinimum <arg> Minimum angle [double] (required, default=-30.0)
-inMultiple <arg> Multiple of tolerance to bracket the minimum
[integer] (required, default=10)
-inNumber <arg> Number of iterations [integer] (required,
default=2)
-inNumber2 <arg> Number of minima from Level 8 to test at Level 4
[integer] (required, default=3)
-inOutput <arg> Output interpolation [option:Trilinear|Bspline
3rd order|Bspline 4th order|Cubic
Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc|Nearest Neighbor]
(required, default=Trilinear)
-inReference <arg> Reference Weighted volume [file] (optional)
-inRegistration <arg> Registration interpolation
[option:Trilinear|Bspline 3rd order|Bspline 4th
order|Cubic Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc] (required,
default=Trilinear)
-inSkip <arg> Skip multilevel search (Assume images are close
to alignment) [boolean] (required, default=false)
-inSource <arg> Source Volumes [file collection: semi-colon
delimited list] (required, default=)
-inSubsample <arg> Subsample image for speed [boolean] (required,
default=true)
-inTarget <arg> Target volume [file] (required)
-inUse <arg> Use the max of the min resolutions of the two
datasets when resampling [boolean] (required,
default=true)
-outExecution Execution Time [string] (required)
-outRegistered Registered Volumes [file collection: semi-colon
delimited list] (required, default=)
-outTransformation Transformation Matrix [matrix semi-colon
delimited rows in text] (optional)
-outTransformation2 Transformation Matrices [file] (optional)
-outTransformations Transformations [file collection: semi-colon
delimited list] (required, default=)
-xDir <arg> Request Output: Processing Directory (default
current) [directory] (optional)
-xFile <arg> Request Output: Results File (default output.txt)
[file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/
</pre>
<li> These features will be released in the next version of JIST.
</ul>

'''Framework for Interoperability of Neuroimaging Software'''
<ul>
<li>Existing Slicer CLI can be bridge to ''almost'' any command line system through use of shell scripts.
<li>These scripts are platform specific and are complex to extend for larger projects --- do we write script factories? Factories for platform specific factories?
<li>If we are going to address the problem of inter-communication, perhaps it would be best to develop a SIMPLE architecture agnostic XML syntax for functionality query, programmatic direction, and result response.
<li>Started a NITRC project (FOPA - Framework for Open Programmatic Access) to develop multi-platform reference implementations. http://www.nitrc.org/projects/fopa/
</ul>
==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-25T15:58:07Z

Bennett:

__NOTOC__
<gallery>

Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
<ul>
<li>Surveyed existing CLI interface and identified areas for extension
<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
<li>Communicated with XIP team about generating a common/compatible interface layer
</ul>
''See detailed results below.''

</div>
</div>

<div style="width: 970%; float: left;">

==Results==
'''Areas for Investigation with CLI and Existing Limitations'''
<ul>
<li>Multiple “programs” per executable.
<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
<li>Report to both stdout (via xml markup) [optional]
<li>Generalize the calling syntax --- especially the ability to control argument structure.
<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
<li>Provide preferred and supported format syntax for resource (file) based communication.
<li>Ability to model dependencies between flags
<li>Workflow level perspective – “sample a bunch of points” = harness level things
<li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
</ul>

'''JIST/MIPAV->CLI Bridge'''
<ul>
<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
<li><pre>
Adding Noise edu.jhu.bme.smile.demo.AddingNoise
Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting
Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra
Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic
Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVol
Demo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo
staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo
...
</pre>

<li> Automated self-documenting executables
<li><pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
[-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
<arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
[-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
[-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
[-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
[-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
[-outExecution] [-outRegistered] [-outTransformation]
[-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
<arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
-h,--help Print this message.
-inApply <arg> Apply rotation [option:All|X|Y|Z] (required,
default=All)
-inCoarse <arg> Coarse angle increment [double] (required,
default=15.0)
-inCost <arg> Cost function [option:Correlation ratio|Least
squares|Normalized cross correlation|Normalized
mutual information] (required,
default=Correlation ratio)
-inDegrees <arg> Degrees of freedom [option:Rigid - 6|Global
rescale - 7|Specific rescale - 9|Affine - 12]
(required, default=Affine - 12)
-inFine <arg> Fine angle increment [double] (required,
default=6.0)
-inInput <arg> Input Weighted volume [file] (optional)
-inMaximum <arg> Maximum angle [double] (required, default=30.0)
-inMinimum <arg> Minimum angle [double] (required, default=-30.0)
-inMultiple <arg> Multiple of tolerance to bracket the minimum
[integer] (required, default=10)
-inNumber <arg> Number of iterations [integer] (required,
default=2)
-inNumber2 <arg> Number of minima from Level 8 to test at Level 4
[integer] (required, default=3)
-inOutput <arg> Output interpolation [option:Trilinear|Bspline
3rd order|Bspline 4th order|Cubic
Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc|Nearest Neighbor]
(required, default=Trilinear)
-inReference <arg> Reference Weighted volume [file] (optional)
-inRegistration <arg> Registration interpolation
[option:Trilinear|Bspline 3rd order|Bspline 4th
order|Cubic Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc] (required,
default=Trilinear)
-inSkip <arg> Skip multilevel search (Assume images are close
to alignment) [boolean] (required, default=false)
-inSource <arg> Source Volumes [file collection: semi-colon
delimited list] (required, default=)
-inSubsample <arg> Subsample image for speed [boolean] (required,
default=true)
-inTarget <arg> Target volume [file] (required)
-inUse <arg> Use the max of the min resolutions of the two
datasets when resampling [boolean] (required,
default=true)
-outExecution Execution Time [string] (required)
-outRegistered Registered Volumes [file collection: semi-colon
delimited list] (required, default=)
-outTransformation Transformation Matrix [matrix semi-colon
delimited rows in text] (optional)
-outTransformation2 Transformation Matrices [file] (optional)
-outTransformations Transformations [file collection: semi-colon
delimited list] (required, default=)
-xDir <arg> Request Output: Processing Directory (default
current) [directory] (optional)
-xFile <arg> Request Output: Results File (default output.txt)
[file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/
</pre>
<li> These features will be released in the next version of JIST.
</ul>

'''Framework for Interoperability of Neuroimaging Software'''
<ul>
<li>Existing Slicer CLI can be bridge to ''almost'' any command line system through use of shell scripts.
<li>These scripts are platform specific and are complex to extend for larger projects --- do we write script factories? Factories for platform specific factories?
<li>If we are going to address the problem of inter-communication, perhaps it would be best to develop a SIMPLE architecture agnostic XML syntax for functionality query, programmatic direction, and result response.
<li>Started a NITRC project (FOPA - Framework for Open Programmatic Access) to develop multi-platform reference implementations. http://www.nitrc.org/projects/fopa/
</ul>
==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-25T15:56:32Z

Bennett:

__NOTOC__
<gallery>

Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
<ul>
<li>Surveyed existing CLI interface and identified areas for extension
<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
<li>Communicated with XIP team about generating a common/compatible interface layer
</ul>
''See detailed results below.''

</div>
</div>

<div style="width: 970%; float: left;">

==Results==
'''Areas for Investigation with CLI and Existing Limitations'''
<ul>
<li>Multiple “programs” per executable.
<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
<li>Report to both stdout (via xml markup) [optional]
<li>Generalize the calling syntax --- especially the ability to control argument structure.
<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
<li>Provide preferred and supported format syntax for resource (file) based communication.
<li>Ability to model dependencies between flags
<li>Workflow level perspective – “sample a bunch of points” = harness level things
<li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
</ul>

'''JIST/MIPAV->CLI Bridge'''
<ul>
<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
<li><pre>
Adding Noise edu.jhu.bme.smile.demo.AddingNoise
Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting
Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra
Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic
Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVol
Demo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo
staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo
...
</pre>

<li> Automated self-documenting executables
<li><pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
[-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
<arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
[-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
[-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
[-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
[-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
[-outExecution] [-outRegistered] [-outTransformation]
[-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
<arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
-h,--help Print this message.
-inApply <arg> Apply rotation [option:All|X|Y|Z] (required,
default=All)
-inCoarse <arg> Coarse angle increment [double] (required,
default=15.0)
-inCost <arg> Cost function [option:Correlation ratio|Least
squares|Normalized cross correlation|Normalized
mutual information] (required,
default=Correlation ratio)
-inDegrees <arg> Degrees of freedom [option:Rigid - 6|Global
rescale - 7|Specific rescale - 9|Affine - 12]
(required, default=Affine - 12)
-inFine <arg> Fine angle increment [double] (required,
default=6.0)
-inInput <arg> Input Weighted volume [file] (optional)
-inMaximum <arg> Maximum angle [double] (required, default=30.0)
-inMinimum <arg> Minimum angle [double] (required, default=-30.0)
-inMultiple <arg> Multiple of tolerance to bracket the minimum
[integer] (required, default=10)
-inNumber <arg> Number of iterations [integer] (required,
default=2)
-inNumber2 <arg> Number of minima from Level 8 to test at Level 4
[integer] (required, default=3)
-inOutput <arg> Output interpolation [option:Trilinear|Bspline
3rd order|Bspline 4th order|Cubic
Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc|Nearest Neighbor]
(required, default=Trilinear)
-inReference <arg> Reference Weighted volume [file] (optional)
-inRegistration <arg> Registration interpolation
[option:Trilinear|Bspline 3rd order|Bspline 4th
order|Cubic Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc] (required,
default=Trilinear)
-inSkip <arg> Skip multilevel search (Assume images are close
to alignment) [boolean] (required, default=false)
-inSource <arg> Source Volumes [file collection: semi-colon
delimited list] (required, default=)
-inSubsample <arg> Subsample image for speed [boolean] (required,
default=true)
-inTarget <arg> Target volume [file] (required)
-inUse <arg> Use the max of the min resolutions of the two
datasets when resampling [boolean] (required,
default=true)
-outExecution Execution Time [string] (required)
-outRegistered Registered Volumes [file collection: semi-colon
delimited list] (required, default=)
-outTransformation Transformation Matrix [matrix semi-colon
delimited rows in text] (optional)
-outTransformation2 Transformation Matrices [file] (optional)
-outTransformations Transformations [file collection: semi-colon
delimited list] (required, default=)
-xDir <arg> Request Output: Processing Directory (default
current) [directory] (optional)
-xFile <arg> Request Output: Results File (default output.txt)
[file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/
</pre>
<li> These features will be released in the next version of JIST.
</ul>

'''Framework for Interoperability of Neuroimaging Software'''
<ul>
<li>Existing Slicer CLI can be bridge to ''almost'' any command line system through use of shell scripts.
<li>These scripts are platform specific and are complex to extend for larger projects --- do we write script factories? Factories for platform specific factories?
<li>If we are going to address the problem of inter-communication, perhaps it would be best to develop a SIMPLE architecture agnostic XML syntax for functionality query, programmatic direction, and result response.
<li>Started a NITRC project (FOPA - Framework for Open Programmatic Access) to develop multi-platform reference implementations. http://www.nitrc.org/projects/fopa/
<ul>
==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-25T15:39:42Z

Bennett:

__NOTOC__
<gallery>

Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
<ul>
<li>Surveyed existing CLI interface and identified areas for extension
<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
<li>Communicated with XIP team about generating a common/compatible interface layer
</ul>
''See detailed results below.''

</div>
</div>

<div style="width: 970%; float: left;">

==Results==
Areas for Investigation with CLI and Existing Limitations
<ul>
<li>Multiple “programs” per executable.
<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
<li>Report to both stdout (via xml markup) [optional]
<li>Generalize the calling syntax --- especially the ability to control argument structure.
<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
<li>Provide preferred and supported format syntax for resource (file) based communication.
<li>Ability to model dependencies between flags
<li>Workflow level perspective – “sample a bunch of points” = harness level things
<li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
</ul>

JIST/MIPAV->CLI Bridge
<ul>
<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
<li><pre>
Adding Noise edu.jhu.bme.smile.demo.AddingNoise
Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting
Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra
Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic
Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVolDemo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo
staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo
...
</pre>

<li> Automated self-documenting executables
<li><pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
[-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
<arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
[-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
[-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
[-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
[-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
[-outExecution] [-outRegistered] [-outTransformation]
[-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
<arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
-h,--help Print this message.
-inApply <arg> Apply rotation [option:All|X|Y|Z] (required,
default=All)
-inCoarse <arg> Coarse angle increment [double] (required,
default=15.0)
-inCost <arg> Cost function [option:Correlation ratio|Least
squares|Normalized cross correlation|Normalized
mutual information] (required,
default=Correlation ratio)
-inDegrees <arg> Degrees of freedom [option:Rigid - 6|Global
rescale - 7|Specific rescale - 9|Affine - 12]
(required, default=Affine - 12)
-inFine <arg> Fine angle increment [double] (required,
default=6.0)
-inInput <arg> Input Weighted volume [file] (optional)
-inMaximum <arg> Maximum angle [double] (required, default=30.0)
-inMinimum <arg> Minimum angle [double] (required, default=-30.0)
-inMultiple <arg> Multiple of tolerance to bracket the minimum
[integer] (required, default=10)
-inNumber <arg> Number of iterations [integer] (required,
default=2)
-inNumber2 <arg> Number of minima from Level 8 to test at Level 4
[integer] (required, default=3)
-inOutput <arg> Output interpolation [option:Trilinear|Bspline
3rd order|Bspline 4th order|Cubic
Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc|Nearest Neighbor]
(required, default=Trilinear)
-inReference <arg> Reference Weighted volume [file] (optional)
-inRegistration <arg> Registration interpolation
[option:Trilinear|Bspline 3rd order|Bspline 4th
order|Cubic Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc] (required,
default=Trilinear)
-inSkip <arg> Skip multilevel search (Assume images are close
to alignment) [boolean] (required, default=false)
-inSource <arg> Source Volumes [file collection: semi-colon
delimited list] (required, default=)
-inSubsample <arg> Subsample image for speed [boolean] (required,
default=true)
-inTarget <arg> Target volume [file] (required)
-inUse <arg> Use the max of the min resolutions of the two
datasets when resampling [boolean] (required,
default=true)
-outExecution Execution Time [string] (required)
-outRegistered Registered Volumes [file collection: semi-colon
delimited list] (required, default=)
-outTransformation Transformation Matrix [matrix semi-colon
delimited rows in text] (optional)
-outTransformation2 Transformation Matrices [file] (optional)
-outTransformations Transformations [file collection: semi-colon
delimited list] (required, default=)
-xDir <arg> Request Output: Processing Directory (default
current) [directory] (optional)
-xFile <arg> Request Output: Results File (default output.txt)
[file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/

</pre>
</ul>

==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-25T15:38:06Z

Bennett:

__NOTOC__
<gallery>

Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER command line interface (CLI) will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
<ul>
<li>Surveyed existing CLI interface and identified areas for extension
<li>Implemented prototype JIST/MIPAV->CLI bridge and discovery procedure.
<li>Circulated drafts of revised "meta-protocol" layer for adaptation between existing CLI
<li>Communicated with XIP team about generating a common/compatible interface layer
</ul>
''See detailed results below.''

</div>
</div>

<div style="width: 970%; float: left;">

==Results==
Areas for Investigation with CLI and Existing Limitations
<ul>
<li>Multiple “programs” per executable.
<li>De-couple dependence of executable query (program which is called with “—xml") from the executable which implements desired functionality.
<li>Provide a mechanism to report non-resource (file-base) results, such as integer, vectors, etc.
<li>Report to both stdout (via xml markup) [optional]
<li>Generalize the calling syntax --- especially the ability to control argument structure.
<li>Allow authors to provide more meta-information about the algorithm (which may be ignored).
<li>Enable the concept of an “ignorable” parameter which need not be understood to use the program.
<li>Increase structure for information that authors can provide about their algorithms and moved this to a separate category.
<li>Increase documentation for “type-of” arguments. Attempted to provide more clarity on a “data-centric” view of the data rather than how these would be represented in ITK/VTK.
<li>Provide preferred and supported format syntax for resource (file) based communication.
<li>Ability to model dependencies between flags
<li>Workflow level perspective – “sample a bunch of points” = harness level things
<li>Ability to have variable number of output arguments and determine the number / names at RUNTIME
</ul>

JIST/MIPAV->CLI Bridge
<ul>
<li> Automated discovery of JIST/MIPAV algorithms from the command line: edu.jhu.ece.iacl.jist.cli.discover
<ul>
<li>Adding Noise edu.jhu.bme.smile.demo.AddingNoise
<il>Chebyshev Fitting edu.jhu.bme.smile.demo.ChebyShevFitting
<il>Demo3: Image Algebra edu.jhu.bme.smile.demo.ImageAlgebra
<il>Image Arithmetic edu.jhu.bme.smile.demo.ImageArithmetic
<il>Demo2: Generate Random Volumes edu.jhu.bme.smile.demo.RandomVol
<il>Demo4: Scale input image edu.jhu.bme.smile.demo.ScaleImageDemo
<il>staple edu.jhu.bme.smile.demo.SmileAlgorithmDemo
<il>...
</ul>
<li> Automated self-documenting executables
<ul>
<li><pre>usage: edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
[-h] [-inApply <arg>] [-inCoarse <arg>] [-inCost <arg>] [-inDegrees
<arg>] [-inFine <arg>] [-inInput <arg>] [-inMaximum <arg>]
[-inMinimum <arg>] [-inMultiple <arg>] [-inNumber <arg>]
[-inNumber2 <arg>] [-inOutput <arg>] [-inReference <arg>]
[-inRegistration <arg>] [-inSkip <arg>] [-inSource <arg>]
[-inSubsample <arg>] [-inTarget <arg>] [-inUse <arg>]
[-outExecution] [-outRegistered] [-outTransformation]
[-outTransformation2] [-outTransformations] [-xDir <arg>] [-xFile
<arg>]

Optimized Automatic Linear Registration 1.1.1.1 1.1.1.1 unk
Linear Registration algorithm based on FLIRT.
-h,--help Print this message.
-inApply <arg> Apply rotation [option:All|X|Y|Z] (required,
default=All)
-inCoarse <arg> Coarse angle increment [double] (required,
default=15.0)
-inCost <arg> Cost function [option:Correlation ratio|Least
squares|Normalized cross correlation|Normalized
mutual information] (required,
default=Correlation ratio)
-inDegrees <arg> Degrees of freedom [option:Rigid - 6|Global
rescale - 7|Specific rescale - 9|Affine - 12]
(required, default=Affine - 12)
-inFine <arg> Fine angle increment [double] (required,
default=6.0)
-inInput <arg> Input Weighted volume [file] (optional)
-inMaximum <arg> Maximum angle [double] (required, default=30.0)
-inMinimum <arg> Minimum angle [double] (required, default=-30.0)
-inMultiple <arg> Multiple of tolerance to bracket the minimum
[integer] (required, default=10)
-inNumber <arg> Number of iterations [integer] (required,
default=2)
-inNumber2 <arg> Number of minima from Level 8 to test at Level 4
[integer] (required, default=3)
-inOutput <arg> Output interpolation [option:Trilinear|Bspline
3rd order|Bspline 4th order|Cubic
Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc|Nearest Neighbor]
(required, default=Trilinear)
-inReference <arg> Reference Weighted volume [file] (optional)
-inRegistration <arg> Registration interpolation
[option:Trilinear|Bspline 3rd order|Bspline 4th
order|Cubic Lagrangian|Quintic Lagrangian|Heptic
Lagrangian|Windowed sinc] (required,
default=Trilinear)
-inSkip <arg> Skip multilevel search (Assume images are close
to alignment) [boolean] (required, default=false)
-inSource <arg> Source Volumes [file collection: semi-colon
delimited list] (required, default=)
-inSubsample <arg> Subsample image for speed [boolean] (required,
default=true)
-inTarget <arg> Target volume [file] (required)
-inUse <arg> Use the max of the min resolutions of the two
datasets when resampling [boolean] (required,
default=true)
-outExecution Execution Time [string] (required)
-outRegistered Registered Volumes [file collection: semi-colon
delimited list] (required, default=)
-outTransformation Transformation Matrix [matrix semi-colon
delimited rows in text] (optional)
-outTransformation2 Transformation Matrices [file] (optional)
-outTransformations Transformations [file collection: semi-colon
delimited list] (required, default=)
-xDir <arg> Request Output: Processing Directory (default
current) [directory] (optional)
-xFile <arg> Request Output: Results File (default output.txt)
[file] (optional)

Provided by: JIST (Java Image Science Toolkit) Command Line Interface v0.1
http://www.nitrc.org/projects/jist/

</pre>
</ul>

==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-22T18:59:02Z

Bennett:

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-22T18:50:23Z

Bennett:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Example: Fully automatic surface, DTI, and sub-cortical analysis
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER CLI interface will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
To be filled in later.

</div>
</div>

<div style="width: 970%; float: left;">

==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-22T18:49:59Z

Bennett:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
Image:JIST-3D.png|Fully automatic surface, DTI, and sub-cortical analysis
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER CLI interface will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
To be filled in later.

</div>
</div>

<div style="width: 970%; float: left;">

==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

File:JIST-3D.png

2009-06-22T18:49:23Z

Bennett:

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-22T17:43:29Z

Bennett:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Core and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER CLI interface will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
To be filled in later.

</div>
</div>

<div style="width: 970%; float: left;">

==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-22T17:40:41Z

Bennett:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
Image:JSIT-fig2.png|JIST Pipeline
Image:JIST-fig3.png|Multi-Code and Grid Processing
Image:JIST-fig1.png|MIPAV Plugins
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER CLI interface will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
To be filled in later.

</div>
</div>

<div style="width: 970%; float: left;">

==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

File:JIST-fig1.png

2009-06-22T17:40:25Z

Bennett:

File:JIST-fig3.png

2009-06-22T17:40:11Z

Bennett:

File:JSIT-fig2.png

2009-06-22T17:38:16Z

Bennett:

File:Fig2.tif

2009-06-22T17:34:40Z

Bennett:

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-22T16:58:03Z

Bennett:

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* GE Research: Jim Miller
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER CLI interface will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
To be filled in later.

</div>
</div>

<div style="width: 970%; float: left;">

==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

Summer2009:Extension of the Command Line XML Syntax/Interface

2009-06-06T18:05:23Z

Bennett: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page </gallery> ==Key Investigators== * Johns Hopkins/Vanderbilt: Bennett Landman * John...'

__NOTOC__
<gallery>
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
</gallery>

==Key Investigators==
* Johns Hopkins/Vanderbilt: Bennett Landman
* Johns Hopkins: Heba Mustufa (not attending in person)

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

<h3>Objective</h3>
We will extend the command line interface (CLI) to support more robust/generic communication between SLICER and third party modules. The primary object is to enable cross-compatibility between the MIPAV/JIST module framework and the SLICER CLI framework. Successful completion of this task would enable the Johns Hopkins CRUISE (cortical surface) and CATNAP (diffusion tensor imaging) modules to be run within SLICER. The secondary (and long term) objective is to establish a flexible and usable syntax for module/plugin communication with graphical front-ends which could be reused in other medical image analysis settings.

</div>

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

<h3>Approach, Plan</h3>
The XML syntax and parser implementation for the SLICER CLI interface will be studied. Recommendations will be made for extended (backward compatible) syntax. A prototype parser for the new schema will be implemented within SLICER.
</div>

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

<h3>Progress</h3>
To be filled in later.

</div>
</div>

<div style="width: 970%; float: left;">

==References==
<ul>
<li>MIPAV: http://mipav.cit.nih.gov/
<li>JIST: http://www.nitrc.org/projects/jist/
<li>SLICER CLI: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
</ul>

</div>

2009 Summer Project Week

2009-06-06T17:56:00Z

Bennett:

Back to [[Project Events]], [[Events]]

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer (Haiying, Ziv, Noby)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|SLicer3, BioImage Suite and Brainlab - Introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)]]
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)]]
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev, C-F Westin)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline (Clement Vachet)]]
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Demo|Demo Brainlab-BioImage Suite-Slicer in BWH OR (Haiying, Isaiah, Nathan Hageman, Haytham)]]
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Xiaodong, Snehashis Roy, Nicole Aucoin)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Fedorov, GeorgiaTech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Fedorov, Marcel, Ron)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan, Andrey Fedorov)
#DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace)
#integration of stereo video into Slicer (Mehdi)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with python]] (Julien de Siebenthal, Sylvain Bouix)
# [[Summer2009:Using_CUDA_for_stochastic_tractography| Developing realtime feedback using CUDA]] (Julien de Siebenthal, Sylvain Bouix)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# [[EM_Segment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)
# Plug-in 3D Viewer based on XIP (Lining)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien de Siebenthal)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)
===CUDA Projects===
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor, Sylvain Jaume, Nicholas, Noby)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-4/#dirlist Slicer-3-4 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH (NA-MIC, NAC, NCIGT)
#Ferenc Jolesz, BWH (NCIGT, NAC)
#Clare Tempany, BWH (NCIGT)
#Tina Kapur, BWH (NA-MIC, NCIGT)
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Randy Gollub, MGH
#Nicole Aucoin, BWH (NA-MIC)
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH (NCIGT)
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH (NAC)
#Haiying Liu BWH (NCIGT)
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH (NA-MIC)
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH (NCIGT)
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH (NA-MIC)
#Sonia Pujol, BWH (NA-MIC)
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH (NAC, NCIGT)
#Lilla Zollei, MGH (NAC)
#Lauren O'Donnell, BWH
#Florin Talos, BWH (NAC)
#Nobuhiko Hata, BWH (NCIGT)
#Alark Joshi, Yale
#Yogesh Rathi, BWH
#Jimi Malcolm, BWH
#Dustin Scheinost, Yale
#Dominique Belhachemi, Yale
#Sam Song, JHU
#Nathan Cho, JHU
#Julien de Siebenthal, BWH
#Peter Savadjiev, BWH
#Carl-Fredrik Westin, BWH
#John Melonakos, AccelerEyes (Wed & Thu morning)
#Yi Gao, Georgia Tech
#Sylvain Bouix, BWH
#Zhexing Liu, UNC-CH
#Eric Melonakos, BWH
#Lei Qin, BWH
#Giovanna Danagoulian, BWH
#Andrew Rausch, BWH (1st day only)
#Haytham Elhawary, BWH
#Jayender Jagadeesan, BWH
#Marek Kubicki, BWH
#Doug Terry, BWH
#Nathan Hageman, LONI (UCLA)
#Dana Peters, Beth Israel Deaconess
#Sun Woo Lee, BWH

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

2009 Summer Project Week

2009-05-08T16:11:50Z

Bennett:

Back to [[Project Events]], [[Events]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation will begin on''' Thursday, April 16th at 3pm ET''', with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([[NA-MIC/Projects/Theme/Template|Wiki Template]])
** 3:30-5:30pm Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]]
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 4D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: TBD
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.

#Prostate Robotics (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#4D Imaging - currently used for Lung Perfusion (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Georgetown?)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#gpu based registration acceleration (James Balter, Greg Sharp, Alark Joshi?, Aditya K., Yogesh Rathi?, Jimi Malcolm, Sandy Wells, Tina Kapur)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Xnat user interface improvements for NA-MIC (Dan M, Tina, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Xnat user clinic - combine with data clinic
#xnat programmer clinic
#Grid Wizard+xnat clinic (Clement)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement, Ipek)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiadong)

IGT Projects:
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#slicer integration of mri compatible prostate biopsy robot(sid, queens)
#breakout session on Dynamic Patient Models (James Balter)
#gpu acceleration of 2d-3d registration (james balter, greg sharp, sandy wells, noby hata, terry peters proxy)

NA-MIC Engineering Projects
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# Using ITK in python (Steve, Demian, Jim)
# VTK 3d Widgets in Slicer3 (Nicole, Will/Karthik)
# Update to Slicer3 Colors module (Nicole)
# EM Segmenter (Sylvain, Nicolas)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# Informatics workflow Design (Wen, Steve, Dan M, Dan B)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 18, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

==Attendee List==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH
#Ferenc Jolesz, BWH
#Clare Tempany, BWH
#Tina Kapur, BWH
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH
#Haiying Liu BWH
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]