NAMIC Wiki - User contributions [en]

DBP3:Iowa

2012-01-11T16:34:20Z

Mscully: /* In Progress / Completed (Reverse Chronological) */

Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]

Engineering Action Plan

=== Overview of the project ===
* http://www.na-mic.org/pages/DBP:HD
* [[2011_Summer_Project_Week_Iowa_Huntington%27s_disease_data_sharing | DBP Data description]]
* [[DBP:HD_Data_Collaborators | Projects using DBP:HD Data]]

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Winter 2012) SPHARM-PDM Slicer3 integration/dissemination
* (In Progress: Winter 2012) Analyze 225 subjects with between 3-6 longitudinally collected scans including Caudate/Putamen/Thalamus using cross sectional tools.
* (Completed: Winter 2011) Implemented in ITKv4: Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
* (Complete: Fall 2011) DTI noise estimation, Rician noise filtering
* (Complete: Fall 2011) DTI pairwise registration (new Slicer module)
* (Complete: Summer 2011) DTI estimation, property map generation
* (Complete: Summer 2011) DTIPrep improvement
* (Complete: Spring 2011) Write Tutorial for DTIPrep
* (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** (Hans Johnson) Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team):
** Word doc Tutorial updated with visual inspection info
** Create Media Wiki version of documentation
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-05-01 (Revised: 2011-10-01) (Clement/Mahshid): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTIprep:
*** Optional Rician LMMSE image filtering - preprocessing
*** Optional Joint Rician LMMSE image filtering - before DTI creation
* 2011-06-24 (Clement/Mahshid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation. Use of XML, extended reporting.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark/Mahshid): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Revised: 2011-10-15) (Clement): DTI pairwise registration (new Slicer module)
** Develop pairwise registration module allowing:
*** Scalar feature (e.g FA) to drive the registration of a DTI image
*** Optional: Direct registration of the DTI image? (DTITK)
** Slicer3-compatible module currently available on NITRC: [http://www.nitrc.org/projects/dtireg/ DTI-Reg]
*** Registration/Warping available via BRAINS (BRAINSFit/BRAINSDemonWarp) and via ANTS (Advanced Normalization Tools)
** Investigate if both scalars and higher models can both be supported.
** Optional: Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite, alternative would be open source AtlasWorks
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for batch processing a large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools
** SPHARM shape summary tool
** Statistical Shape Analysis Tools
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

DBP3:Iowa

2012-01-11T16:25:27Z

Mscully: /* In Progress / Completed (Reverse Chronological) */

Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]

Engineering Action Plan

=== Overview of the project ===
* http://www.na-mic.org/pages/DBP:HD
* [[2011_Summer_Project_Week_Iowa_Huntington%27s_disease_data_sharing | DBP Data description]]
* [[DBP:HD_Data_Collaborators | Projects using DBP:HD Data]]

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Winter 2012) SPHARM-PDM Slicer3 integration/dissemination
* (Completed: Winter 2011) Implemented in ITKv4: Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
* (Complete: Fall 2011) DTI noise estimation, Rician noise filtering
* (Complete: Fall 2011) DTI pairwise registration (new Slicer module)
* (Complete: Summer 2011) DTI estimation, property map generation
* (Complete: Summer 2011) DTIPrep improvement
* (Complete: Spring 2011) Write Tutorial for DTIPrep
* (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** (Hans Johnson) Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team):
** Word doc Tutorial updated with visual inspection info
** Create Media Wiki version of documentation
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-05-01 (Revised: 2011-10-01) (Clement/Mahshid): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTIprep:
*** Optional Rician LMMSE image filtering - preprocessing
*** Optional Joint Rician LMMSE image filtering - before DTI creation
* 2011-06-24 (Clement/Mahshid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation. Use of XML, extended reporting.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark/Mahshid): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Revised: 2011-10-15) (Clement): DTI pairwise registration (new Slicer module)
** Develop pairwise registration module allowing:
*** Scalar feature (e.g FA) to drive the registration of a DTI image
*** Optional: Direct registration of the DTI image? (DTITK)
** Slicer3-compatible module currently available on NITRC: [http://www.nitrc.org/projects/dtireg/ DTI-Reg]
*** Registration/Warping available via BRAINS (BRAINSFit/BRAINSDemonWarp) and via ANTS (Advanced Normalization Tools)
** Investigate if both scalars and higher models can both be supported.
** Optional: Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite, alternative would be open source AtlasWorks
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for batch processing a large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools
** SPHARM shape summary tool
** Statistical Shape Analysis Tools
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-11-07T15:17:12Z

Mscully: /* Data Files */ Added ANN thesis and presentation.

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:NAMIC_HD_Xnat_Interface.png|Screenshot of xnat interface for NAMIC_HD project
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UIowa: Hans Johson, Mark Scully

==Data Files==
*[[File:Anonymized_factorsExternalIDs_with_blage_mriDate_scanID_daysSince.xlsx]]
*[[File:NAMIC%2BFactors.doc]]
*[[File:NAMIC_HD_DWI_DTI.xlsx]]
*[[File:NAMIC_HD_DataDescription.pdf]]
*[[File:ANN_Segmentation_thesis.pdf]]
*[[File:20111102_ANNSegmentation.pptx]]

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

<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

</div>

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

<h3>Approach, Plan</h3>
Data will be made available via xnat.

</div>

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

<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.

Fill out the form [[File:NAMIC_DATA_SHARING.doc]] to request access.

In addition to the raw data anonymized factors relating to the disease and three different reconstructions have been made available. The anonymized factors are available in the File:NAMIC_HD_DataDescription.pdf file in the data files section above. The first reconstruction is the output of the BRAINS AutoWorkup pipeline run in June. The second is the pipeline run 2011-09 with improved segementations. The third is the DWI data after processing. The reconstructions are explained in the above data files.

After access has been granted and an account has been created you can fetch the raw data using the script [[File:Fetch_NAMIC_HD_data.sh.gz]] and the processed data using [[File:Fetch_NAMIC_HD_derived_data.sh.gz]].

The raw data is large (over 1TB) so it will take a long time and require a large amount of space.

Run either script with '-h' for terse help. Each file takes a basePath under which the output will be constructed of the form $basePath/NAMIC_HD/subjectID/scanID.zip for the raw data and $basePath/NAMIC_HD/subjectID/scanID_type.zip for the processed data. The raw data zip files expand to scanID/scans/scanTypes/resources/DICOM/files/ and the processed zip files expand to scanID/reconstructions/scanID_10_AUTO.NN3Tv20110419-BRAINSAutoWorkup/out/resources/resourceType/files/. When fetching the raw data you can specify a list of image types you are interested in using '-t' followed by a comma delimited list of scan types (It defaults to 'ALL'). You can get a list of possible scan types by running "./Fetch_NAMIC_HD_DATA.sh -l". The types you are likely to be interested in are at the beginning of the list. If either script is interrupted while running it can be restarted and it will skip over already downloaded zip files (provided you have not set force=True or deleted the relevant .zip files). If you run either command without a required input you will be prompted to provide it. Brief usage examples for each command follows:

usage: ./fetch_NAMIC_HD_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-l (list) List scan types and exit.<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>
-t scanTypes: comma delimited list of scan types. (Defaults to ALL) Ex: T1-30,T2-30<br>

usage: ./fetch_NAMIC_HD_derived_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>

</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat

File:20111102 ANNSegmentation.pptx

2011-11-07T15:16:42Z

Mscully: Eun Young Kim's presentation on Artificial Neural Network Segmentation of neural anatomical structures.

Eun Young Kim's presentation on Artificial Neural Network Segmentation of neural anatomical structures.

File:ANN Segmentation thesis.pdf

2011-11-07T15:15:20Z

Mscully: Eun Young Kim's thesis on Artificial Neural Network (ANN) segmentation of neural anatomical structures.

Eun Young Kim's thesis on Artificial Neural Network (ANN) segmentation of neural anatomical structures.

DBP3:Iowa

2011-11-04T20:41:24Z

Mscully: /* Overview of the project */

Back to [[DBP3:Main|NA-MIC DBPs]] | [[Cores|NA-MIC Cores]]

Engineering Action Plan

=== Overview of the project ===
* http://www.na-mic.org/pages/DBP:HD
* [[2011_Summer_Project_Week_Iowa_Huntington%27s_disease_data_sharing | DBP Data description]]
* [[DBP:HD_Data_Collaborators | Projects using DBP:HD Data]]

=== In Progress / Completed (Reverse Chronological) ===

* (Complete: Fall 2011) DTI noise estimation, Rician noise filtering
* (In Progress: Fall 2011) DTI pairwise registration (new Slicer module)
* (In Progress: Fall 2011) SPHARM-PDM Slicer3 integration/dissemination
* (In Progress: Fall 2011) Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
* (Complete: Summer 2011) DTI estimation, property map generation
* (Complete: Summer 2011) DTIPrep improvement
* (Complete: Spring 2011) Write Tutorial for DTIPrep
* (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** (Hans Johnson) Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team):
** Word doc Tutorial updated with visual inspection info
** Create Media Wiki version of documentation
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-05-01 (Revised: 2011-10-01) (Clement/Mahshid): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTIprep:
*** Optional Rician LMMSE image filtering - preprocessing
*** Optional Joint Rician LMMSE image filtering - before DTI creation
* 2011-06-24 (Clement/Mahshid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation. Use of XML, extended reporting.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark/Mahshid): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Revised: 2011-10-15) (Clement): DTI pairwise registration (new Slicer module)
** Develop pairwise registration module allowing:
*** Scalar feature (e.g FA) to drive the registration of a DTI image
*** Direct registration of the DTI image (DTITK?)
** First release of Slicer3-compatible module currently available on github: [https://github.com/clementsan/DTI-Reg DTI-Reg]
** Investigate if both scalars and higher models can both be supported.
** Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite, alternative would be open source AtlasWorks
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for batch processing a large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools
** SPHARM shape summary tool
** Statistical Shape Analysis Tools
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

DBP:HD Data Collaborators

2011-11-04T20:31:50Z

Mscully: Created page with '{| class="wikitable" |- ! Requester ! Institution ! Description of Project |- | Ramesh Sridharan & Adrian Dalca | Polina Gollard's Group, CSAIL, MIT | Learn image manifolds and t…'

{| class="wikitable"
|-
! Requester
! Institution
! Description of Project
|-
| Ramesh Sridharan & Adrian Dalca
| Polina Gollard's Group, CSAIL, MIT
| Learn image manifolds and the underlying structure of brain images by incorporating external constraints such as longitudinal data.
|-
| Archana Venkataraman
| Polina Gollard's Group, CSAIL, MIT
| Model the structural-functional relationship in the brain and how it breaks down in clinical populations.
|-
| Manasi Datar & Ross Whitaker
| SCI Institue, School of Computing, University of Utah
| Include longitudinal shape regression into the ShapeWorks framework.
|-
| Martin Styner
| University of North Carolina
| novel longitudinal shape analysis methodology and apply those to the longitudinal changes of the nucleus caudate in patients suffering from Huntington’s disease, as well as novel longitudinal DTI assessment methods and apply those to several white matter fiber tracts of interest, such as the cerebro spinal tract and anterior thalamic radiations, in patients suffering from Huntigton’s disease.
|-
| Yi Gao
| Georgia Tech
| Segmentation and registration research.
|-
| Guido Gerig
| University of Utah
| Develop analysis methodologies for 4D MR images, specifically quantifying longitudinal anatomical changes and comparing such changes between different populations.
|-
| Carl-Fredrik Westin
| Brigham and Women's Hospital / Harvard Medical School
| Develop novel analysis methods.
|-
| Thomas Shultz
| Max Plank Institute
| Develop reliable and reproducible methods for in vivo segmentation of thalamic subnuclei.
|-
| William Wells
| Brigham and Women's Hospital / Harvard Medical School
| Evaluate quantitative susceptibility mapping.
|-
| Hans Johnson
| University of Iowa
| Developing new and refined existing tools to achieve the specific aims of the NA-MIC HD-DBP.
|-
| Casey Goodlett
| Kitware
| Develop registration algorithms for distribution in Slicer 3D.
|-
| Dan Marcus
| Washington University in St. Louis School of Medicine
| Improve data distribution and modeling methods for the xnat imaging informatics platform.
|-
| Anuj Srivastava and Sentibaleng Ncube
| Florida State University
| Development of novel Riemannian metrics for HARDI data analysis.
|-
| Stefan Klöppel & Volkmar Glauche
| UNIVERSITÄTS FREIBURG
| Study white matter changes in different stages of HD and compare data variability between diffusion directions for sequences with many direction but a single repetition.
|-
| Jessica Turner
| University of California, Irvine
| Develop the use of automated reasoning systems to represent the connectivity of white matter tracts.
|-
| Xiaodong Tao
| GE Global Research Center
| Improve the DicomToNrrd diffusion tensor conversion tool, and improve 3D Slicer (www.slicer.org) DTI analysis processing
|-
| Zhexing Liu
| The University of North Carolina at Chapel Hill
| Improve the DTIPrep diffusion tensor quality control tool.
|}

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-10-12T21:50:42Z

Mscully: /* Data Files */ Added DataDescription pdf and text describing new data.

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:NAMIC_HD_Xnat_Interface.png|Screenshot of xnat interface for NAMIC_HD project
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UIowa: Hans Johson, Mark Scully

==Data Files==
*[[File:Anonymized_factorsExternalIDs_with_blage_mriDate_scanID_daysSince.xlsx]]
*[[File:NAMIC%2BFactors.doc]]
*[[File:NAMIC_HD_DWI_DTI.xlsx]]
*[[File:NAMIC_HD_DataDescription.pdf]]

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

<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

</div>

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

<h3>Approach, Plan</h3>
Data will be made available via xnat.

</div>

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

<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.

Fill out the form [[File:NAMIC_DATA_SHARING.doc]] to request access.

In addition to the raw data anonymized factors relating to the disease and three different reconstructions have been made available. The anonymized factors are available in the File:NAMIC_HD_DataDescription.pdf file in the data files section above. The first reconstruction is the output of the BRAINS AutoWorkup pipeline run in June. The second is the pipeline run 2011-09 with improved segementations. The third is the DWI data after processing. The reconstructions are explained in the above data files.

After access has been granted and an account has been created you can fetch the raw data using the script [[File:Fetch_NAMIC_HD_data.sh.gz]] and the processed data using [[File:Fetch_NAMIC_HD_derived_data.sh.gz]].

The raw data is large (over 1TB) so it will take a long time and require a large amount of space.

Run either script with '-h' for terse help. Each file takes a basePath under which the output will be constructed of the form $basePath/NAMIC_HD/subjectID/scanID.zip for the raw data and $basePath/NAMIC_HD/subjectID/scanID_type.zip for the processed data. The raw data zip files expand to scanID/scans/scanTypes/resources/DICOM/files/ and the processed zip files expand to scanID/reconstructions/scanID_10_AUTO.NN3Tv20110419-BRAINSAutoWorkup/out/resources/resourceType/files/. When fetching the raw data you can specify a list of image types you are interested in using '-t' followed by a comma delimited list of scan types (It defaults to 'ALL'). You can get a list of possible scan types by running "./Fetch_NAMIC_HD_DATA.sh -l". The types you are likely to be interested in are at the beginning of the list. If either script is interrupted while running it can be restarted and it will skip over already downloaded zip files (provided you have not set force=True or deleted the relevant .zip files). If you run either command without a required input you will be prompted to provide it. Brief usage examples for each command follows:

usage: ./fetch_NAMIC_HD_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-l (list) List scan types and exit.<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>
-t scanTypes: comma delimited list of scan types. (Defaults to ALL) Ex: T1-30,T2-30<br>

usage: ./fetch_NAMIC_HD_derived_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>

</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat

File:NAMIC HD DataDescription.pdf

2011-10-12T21:46:13Z

Mscully: Describes the output of the new autoworkup processing and the DTI processing pipeline.

Describes the output of the new autoworkup processing and the DTI processing pipeline.

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-10-12T21:43:29Z

Mscully: /* Data Files */ Added link to new DWI spreadsheet

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:NAMIC_HD_Xnat_Interface.png|Screenshot of xnat interface for NAMIC_HD project
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UIowa: Hans Johson, Mark Scully

==Data Files==
*[[File:Anonymized_factorsExternalIDs_with_blage_mriDate_scanID_daysSince.xlsx]]
*[[File:NAMIC%2BFactors.doc]]
*[[File:NAMIC_HD_DWI_DTI.xlsx]]

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

<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

</div>

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

<h3>Approach, Plan</h3>
Data will be made available via xnat.

</div>

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

<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.

Fill out the form [[File:NAMIC_DATA_SHARING.doc]] to request access.

After access has been granted and an account has been created you can fetch the raw data using the script [[File:Fetch_NAMIC_HD_data.sh.gz]] and the processed data using [[File:Fetch_NAMIC_HD_derived_data.sh.gz]].

The raw data is large (over 1TB) so it will take a long time and require a large amount of space.

Run either script with '-h' for terse help. Each file takes a basePath under which the output will be constructed of the form $basePath/NAMIC_HD/subjectID/scanID.zip for the raw data and $basePath/NAMIC_HD/subjectID/scanID_type.zip for the processed data. The raw data zip files expand to scanID/scans/scanTypes/resources/DICOM/files/ and the processed zip files expand to scanID/reconstructions/scanID_10_AUTO.NN3Tv20110419-BRAINSAutoWorkup/out/resources/resourceType/files/. When fetching the raw data you can specify a list of image types you are interested in using '-t' followed by a comma delimited list of scan types (It defaults to 'ALL'). You can get a list of possible scan types by running "./Fetch_NAMIC_HD_DATA.sh -l". The types you are likely to be interested in are at the beginning of the list. If either script is interrupted while running it can be restarted and it will skip over already downloaded zip files (provided you have not set force=True or deleted the relevant .zip files). If you run either command without a required input you will be prompted to provide it. Brief usage examples for each command follows:

usage: ./fetch_NAMIC_HD_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-l (list) List scan types and exit.<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>
-t scanTypes: comma delimited list of scan types. (Defaults to ALL) Ex: T1-30,T2-30<br>

usage: ./fetch_NAMIC_HD_derived_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>

</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat

File:NAMIC HD DWI DTI.xlsx

2011-10-12T21:42:36Z

Mscully: Spreadsheet detailing NAMIC_HD shared data anatomical and DWI imaging quality / status.

Spreadsheet detailing NAMIC_HD shared data anatomical and DWI imaging quality / status.

Engineering:TCON 2011

2011-09-08T19:09:21Z

Mscully: /* 2011-09-08 */

Back to [[TCON:Main|TCON:Main]], [[Events]]

__TOC__

== 2011-09-08 ==
Attendees: Ron, Steve, Stephen, Mark, Nicole, JC, J2, Tina, Dominik, Zach Mullen,
*Status Update on Extensions
*Tractography Workshop at MICCAI
* Documentation
** CLI's XML
** ITK Modules
** [[2011_Slicer4-Documentation-Sprint|Oct 20 documentation event]]
* Data Transfer
** DICOM Module (in experimental)
** Data consolidation
*** Tutorials (powerpoint)
*** Image (non-dicom)
*** Upload/download
** DICOM Load Speeds

==2011-09-01==

* Attendees: Mark, Jim, Nicole, Steve, Hans, Stephen

* ITKv4 DICOM. DCMTK plan. Extend schedule. Get DCMTK to build as an external project. SCU and SCP classes have been added to DCMTK 3.6. Make ITK examples that would listen using DCMTK and the process data with ITK. They are not taking on the ownership of DicomToNrrd.
* What about DicomToNrrd? Should it be cleaned up using straight ITK, GDCM, DCMTK, CTK, ...? Hans and Mark will reassess and report back.
* Python mmap availability in Slicer is a blocker for Nipype

==2011-08-25==

* Attendees: Ron, Steve, Daniel, Mark, Jim, Nicole, Julien, Hans

* Topics:
** Review the status of [[Events:Slicer4-Review-07-2011#RSNA_2011_Targeted_Objectives|RSNA targeted action items for Slicer 4]]
** Annotations module goals
** (if time allows) Review of new wiki-module documentation process proposed by JC.
* Notes: (One month until RSNA freeze happens)
** GUI: Need to agree on moc-up of Slicer Views
** Volume Rendering: Started. Working on GPU Memory and Transfer Function.
** Models: Mostly done.
** Editor: "Seems straightforward"
** Welcome Module: Not yet started
** Volumes Module: Can drop some features. Still slow. Unknown time required - risks.
** Tractography: Going well - done, but tweaks
** Sceneview: Might not be possible as scoped - Ron/Nicole to discuss offline
** Annotation: Appearance of annotations, appearance of module, ... - may need to scale-back. Limited resources>
*** See [[Projects:ARRA:miAnnotation:Feedback#General_Changes_.28Target_for_RSNA_release.29 | notes from related meeting]]
** Documentation: JC
** Linking and compare view: Linking - Base behavior in-place; spreading capabilities. Compare-view
** ROIs: going well
** Diffusion MRI: Making good progress
** Hierarchies: Dealing with Qt bug. Annotations need work.
** VTK Bug Fixes: Fixes are in VTK. Remaining aren't critical now (text and bi-dim dropped for RSNA release).
** CTK-DICOM Widget: Data - Almost (3/4 done) Widget - needs testing and packaging
** Optimized displayable manager: Progress being made - backburner project
** Brainsfit: Being integrated. Doesn't work on windows (dll weirdness). Bundling on mac - installation not working.
*** Too complex/unclear how to build external module that doesn't become locked to Slicer
** Annotation Speedup: Coming along - keeping it simple for first implementation
** Extensions: Keeping the number small - enabled on dashboard - just waiting for green dashboard
** Web infrastructure and documentation: wiki templates

==2011-08-18==

Attendees:

*Slicer 4 documentation: [http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0 See here] and [http://wiki.slicer.org/slicerWiki/index.php/Module:EndUserDocumentationTemplate-4.0 here].
* tables and charts in Slicer (Ron)
**We need a viewer as a container for spreadsheets and charts.
**three initial use case scenarios:
# sampling across time in a time series: single pixel, small area
# label statistics: simple descriptive statistics derived from the gray scale image underlying a label map with multiple labels
#statistics along tracts in tractography
* mrml nodes for workflows (Stephen)
** perhaps a mrml node that contains a database.

* Discussion
** For now we will try using the scripted module node and rely on the keyword/value (where value is a string)
** beyond that there are several options for structuring data, but they may need to be driven by concrete use cases
*** possibly HDF5, sqlite, or other bulk data storage data structures
* Volume rendering transfer function - needs antialiasing

==2011-08-11==

Attendees: Ron, Steve, Stephen, Tina, Nicole, Daniel, Mark

*http://www.slicer.org/slicerWiki/index.php/Documentation-4.0

==2011-08-04==

Attendees: Stephen, Mark, Nicole, Tina, Ron

Agenda:
* hans' request re. github/svn pull. (nicole). supported way to do is an svn checkin (Stephen).

==2011-07-28==
Attendees:

Jean-Christophe Fillion-Robin, Sharp, Gregory C., Bill Lorensen, Andriy Fedorov, Dominik Meier, Dominique Belhachemi, Matt McCormick, Mark Scully, Ron Kikinis, Steve Pieper, Demian Wassermann, Tina Kapur, Luping Fang, Hans Johnson

Agenda:
*Moving from ITK3 to [http://www.vtk.org/Wiki/ITK#ITK_Version_4 ITK4]
**Impact to the developer community by the changes in features, API, algorithms
**[[Events:Slicer4-Review-07-2011#RSNA_2011_Targeted_Objectives|Planned Slicer 4.0 release at RSNA 2011]]
**Brainsfit in Slicer4
**[[2011_Winter_Project_Week:_Slicer4-ITK4_Continuous_Integration|Continous Integration of Slicer 4 and ITK 4]]: Some existing work by Bill Lorensen

Decisions:
*RSNA version of Slicer4 will be be based on ITKv3
*January version of Slicer4 will be based on ITKv4
*A parallel build of Slicer4 will be possible during this time frame. There is a possibility that staticly linked executables based on ITKv4 will be made available even when Slicer4 is built with ITKv3
*Ron confirmed his desire to reduce the amount of redundancy in the modules that are available in Slicer4. Hans offered to find redundant versions of tools, and reduce the redundancy.
*There was a discussion about revisiting the IO enhancement that would help reduce memory copy in ITK for performance reasons. There may be other benefits in to the NRRD/NiFTi and other image IO readers that currently copy memory.
**See: [https://github.com/Slicer/ITK/commit/12349021b152ac6546c2caf09bbbee4266baddad]
**See also [http://www.slicer.org/slicerWiki/index.php/ITKv4_Migration_plan#Custom_MetaIO_in_SlicerITK]

==2011-07-15==
Agenda:

* Open Source Software Competition in Korea: http://www.ossaward.org/index.php
* SPL-related web services will be down until tomorrow (mailing lists, sites, wikis, bug tracker...). Slicer svn will remain up (it is hosted at Kitware)

==2011-07-07==
Attendees: Steve, Ron, Luping, Jim, Stephen

* Jim is meeting with Andrey at GE about the prostate compare view use cases
* Discussion of ongoing slicer4 porting issues
** packaging on mac
** scripted displayble manager

==2011-06-30==
Attendees: Steve, Stephen, Tina, Nicole, Daniel, JC, J2, Ron

* Discuss Slicer release schedule (slicer4 and [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues slicer 3.6.4])
**Target Slicer product release for RSNA
**That means end of September at latest, so that there is time to work on documentation, training modules and testing/debugging.
**[[Events:Slicer4-Review-07-2011|Slicer4 Sprint planned for July 19-20 in Boston]]

==2011-06-23==

No phone call due to [[2011_Summer_Project_Week|Project Week]].

==2011-06-16==
Attendees: Xiadong, Tina, Marc, Nicole, Daniel (UPenn), Mohasen, Luping (SPL)

*Working meeting to do documentation: http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers
** [http://www.slicer.org/slicerWiki/index.php/Slicer4:SceneViewsModule Scene Views] updated
** [http://www.slicer.org/slicerWiki/index.php/Slicer4:EMSegment EMSegment] updated
** [http://www.slicer.org/slicerWiki/index.php/Slicer4:VMTK VMTK] updated

==2011-06-09==
Attendees: Jim, Xiadong, Sonia, Dominik, Dominique, Andreas, Ron, Tina, Nicole, Stephen, Mohasen, Mark Scully, Drew Rotham, Steve Pieper

Agenda:
*[http://www.na-mic.org/Wiki/index.php/Summer_2011_Tutorial_Contest 2011 Summer 2011 Tutorial contest ]dead-line extended until June 13
*DICOM projects at summer project week:
** Networking: putting ctk/dcmtk into slicer4; use case scenarios (Nicole, Steve, Noby, +?)
** ITKv4 DICOM Support: what features will be available? (Drew, Steve, Dan, Bill, +?)
** DICOMRT: mapping between RT/ITK/Slicer datastructures (Greg, Steve, Luis)
** DWI DICOM: what will we do without Xiaodong?!? (Xiaodong, Jim, Hans, Demian)
** other topics?
*Discuss the structure of Slicer 4 documentation in preparation for next week [http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0 Slicer 4 documentation placeholder]
*Agenda for next week will be to have a working meeting where appropriate people join the call and spend the hour on Slicer 4 documentation in preparation for project week http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers

==2011-06-02==

Attendees: Jim, Tina, Steve, Stephen, Demian, Szymon, Anthony Blumsfield, Xiaodong, Nicole, Julien, Suarez, Hans Johnson, Mohasen (VA Hospital), Lauren O'Donnell

Agenda:
*DTI projects at summer project week:
**Tractography Projects: http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Diffusion#Features_to_be_addressed_before_the_Summer_NA-MIC_meeting
**http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week#Projects
*Szymon (EPFL)
**OpenIGT interface Slicer and lab robot
*Anthony
**Spine segmentation project
*Mohasen
**

== 2011-05-26==

Attendees: Junichi, Tina, Tamas, Tamas, Stephen, Jim, Noby, Peter Kazanzies, Ehsan Azimi, Greg Fischer, Hao, Suarez, Csaba

* OpenIGTLink at Project Week

==2011-05-19==
Attendee: Jim, Steve, Dominik, Nicole, Xiaodong, Ross, Marc, Tina, Chiara Carminati (Milan), Adrian(MIT), Ramesh(MIT), Clement (UNC), Nadya (MGH)

Agenda:

*http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week
*openIGTLink discussion next week.

==2011-05-12==

Attendees: Tina, Steve, Allen, Clement, Yi, Ivan, Yi Fi Lou, Jim, Stephen, Mark, Nicole,

Algorithm core participants discuss project week.
* RSS as Editor module
* Mass Spect for Brain Tumors (GaTech, NCIGT, BWH collaboration)
* Head and Neck cancer bone registration
* Multi-modality image registration

==2011-05-05==

No t-con.

==2011-04-28==

Agenda:

*Summer Project Week Kickoff -- Engineering Projects
**http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week

==2011-04-21==
Attendees: Steve, Tina, Julien, Xiaodong, Dominik, Marc, Nicole, Dan, Danielle

Agenda:
*Slicer4 windows build question (Steve)
*MGH DBP discussion with Greg Sharp about multilayer treatment plans (Steve).
*visualizing deformation fields via RGB or vector fields via tensor image (Dominik, Steve)
*Since we had some time today, we did a pre-kickoff discussion of engineering projects: [[2011_Summer_Project_Week#Projects]]

==2011-04-14==
Attendees:

Agenda:

* Continue Slicer4 discussion
** Can schedule another call with Extension developers once the Factory is up and running with example extensions - http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Breakout_Slicer#Extensions
** Any objection to removing all KWWidget code from slicer4 svn?
*** Jc: Option Slicer_BUILD_KWWIDGETS is not supported anymore (it means the build system has been cleaned already) Module and GUI folder code are still here though
** Wrapping Module code (MRML and Logic) in python
*** Jc: Already functional. Need to make wrapping works when module are build as extension
*** VTK classes associated with module should be properly exposed in python.
** Check out "what changed?" and "multivolume containers" in the [http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers#Projects list of Slicer 4 projects].
** Speed, Speed, Speed
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:VisualBlog

==2011-04-07==
Attendees: Jim, Steve, Tina, Dominik, Daniel, Nicole, JC, Suares, Demian, Kilian, Stephen, Andras, Tamas, Marc, Julien Finet, Danielle P.

Agenda:

* Slicer4
** Progress on Modules? Review and update of: http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Breakout_Slicer
*** See comments associated with each modules on 2011_Winter_Project_Week:Breakout_Slicer page
** Any objection to removing all KWWidget code from slicer4 svn?
*** Jc: Option Slicer_BUILD_KWWIDGETS is not supported anymore (it means the build system has been cleaned already) Module and GUI folder code are still here though
** Wrapping Module code (MRML and Logic) in python
*** Jc: Already functional. Need to make wrapping works when module are build as extension
*** VTK classes associated with module should be properly exposed in python.
** Check out "what changed?" and "multivolume containers" in the [http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers#Projects list of Slicer 4 projects].
** Speed, Speed, Speed

==2011-03-24==
Attendees: Steve, Jim, Ann, Tina, Daniel, Suares, Marc, Jack, Nicole, Dominique, Ron

Agenda:

*Scientific Progress Report Discussion (Ann Adams will join at 3pm for 20 minutes)
* http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

==2011-03-24==
Attendees: Jim, Ron, Tina, Dominik, Dominique, Marc, Hans, Daniel, Nicole, Curt, Julien

* Slicer4 layouts - [[Media:FirstCompareViewInSlicer4.png|Hey a CompareView]]
* http://wiki.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:LinkedControls
* http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer
* Licensing Question: CMTK/Brainsfit/

==2011-03-17==
Attendees: Jim, Ron, Marc, Tina, Nicole, Xiaodong, Greg, Dave Partika, Julien Finet

Agenda:
*Slicer 3.6.3: 64 bit versions, extensions
*the default location for a lot of slicer things is the user home directory. This should be changed. It causes problems in the SPL.
**where to put it, how to initiate?
*saving Slicer 4 mrml scenes as secondary capture (Ron)
**I would like to be able to save an entire scene as a [http://www.medicalconnections.co.uk/wiki/Creating_Secondary_Capture_Images dicom secondary capture]. This would allow to use accessible pacs systems as repositories for slicer scenes
**is there a way to incorporate thumbnails and descriptions from the new sceneviews?
*Slicer3 linked controls
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:LinkedControls#cite_note-0 Jim's notes]
** [http://www.na-mic.org/Bug/view.php?id=1117 bug 117]

Notes:
* Dave P will build Windows builds of Slicer and extensions (a version without numpy, make a release note) and Steve will upload. Also the darwin, need to match svn version
* Default location: ask user for not home dir directory if default is not set
** related bugs: [http://www.na-mic.org/Bug/view.php?id=598 598]
* Secondary capture to interact with PACS
** tcon before project week with Jim, Nicole, Wendy, Steve to talk about infrastructure
* Linked controls
** Scroll wheel and arrows after Steve/Nicole's implementation of the link/orientation flag only scroll the current slice viewer and the other viewers with the same orientation, need more feedback from users/Andrey
** use cases between move all slices by copying this slices's RAS matrix to the other slice nodes, and linked increment slice that moves the other slices by an incremental distance
** reformat mode and linking. If in compare view mode and change one of multiple reformat slices, the other reformatted slice views will jump to that
** proposal: link some mode, so have more granularity than all or none (currently do have a one slice link toggle key)
*** reserve some link states so can by default link certain slices
* Ron to Xiaodong: use HAMMER on new brain atlas? not tried yet

==2011-03-10==

Attendees: Jim, Steve, Mark S., Nicole, Tina

Agenda:
* 3.6.4 release planning discussion [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues]
** In particular, fix for the linked slice views [http://www.na-mic.org/Bug/view.php?id=1115] (see also [http://www.na-mic.org/Bug/view.php?id=1003 1003])
** pan mode resets slice orientation ([http://www.na-mic.org/Bug/view.php?id=1117 bug #1117])
** What steps should be used for testing fixes for these bugs?
*** Are all use cases covered in currently [http://www.slicer.org/slicerWiki/index.php/Modules:MainApplicationGUI-Documentation-3.6#Linking_Control_of_Slice_Viewers documented behavior]?
***Show hide reformat widget behavior should incorporate the Michal Depa/Steve Pieper modifcations for linked views with reformat widget.
*** What optimizations (delayed updates) are we expected in for situations like compare view?
**when linked views are in the same location and visible, there are artifacts in the 3d viewer.
* More flexibility in the names of the results of CLI's. It would be good to have the ability to incorporate:
**Source volume name
**Module name
**some important parameters

Notes:
* linked slice views: Jim will write up a wiki page describing the expected behaviour, Steve and Nicole will debug
* CLI names: Jim says "yes"
* CLI compilation with separated header files: Jim, Steve, Mark to look into this via webex

==2011-03-03==

Attendees: Steve, Nicole, Jim, Andrey, Suarez, Ron, Stephen A., Daniel H, Dominique B., Xioadong, Greg Sharp, Mark S, Dominik, Hans

Agenda:
* C++/C wrapping of modules
** Hans and Greg figured out what was going wrong. In BRAINS tools they did a trick to get around Bill's trick. It takes 8 minutes to build BRAINSfit, to break it down into smaller compilation units and test it using ITK testing framework. It has a thin wrapper around program to add comparator functions. BRAINSfit is a small 3 line wrapper around BRAINS fit primary that takes argc and argv and includes generated header file. You can't include CLP header file in both compilation units since functions are defined in header file. See error at link time. If you put the right ifdef compiling for slicer and module description is defined you can make it work. Hans would like to see the CLP broken apart into a compile until and a header unit. Jim: harder to build and link - but is done through macros. Could have a test before include CLP.h. Hans: wants to be able to include the .h file in every file. Change: now would have to write a programCLP.h and programCLP.cxx.
** definitely needs to be done in Slicer4, tbd in Slicer3 (Hans using Slicer3 in his class).
*** the add executable, add library lines macros would need to be touched, need to link new object file
*** before when build both a shared and a command line module it would have to rebuild all the itk stuff twice, Casey made the change to not require it
*** Steve: came up wrt diffusion modules because they're using vtk nrrd readers that don't know about shared memory pointers
*** Hans: was building itk files three times for exec, lib, testing
** Jim will take a look at what breaks when try to split it out, code generation is easy, the add_executable will be a bit tricky
** Hans: suggests adding the .cxx to the GenerateCLP macro that defines the .h, to use in the CMakeLists. Hans will do the changes to all the execution modules that need to be changed once the infrastructure is changed (or not).
** One BRAINSfit test failing: any multi threaded mutual information code is suspect to the bug that they found. Quick fix: restrict to one thread, huge slow down (2-4x). Bug is in the Mattes mutual information optimize metric (?) in the registration framework for certain number of threads (4,7, etc). Stephen A will look at it after March 9.
* Annotation module widget priority for ROI nodes
** Ron, Daniel agrees to put it as higher than the bidimensional widget
** ROI widget is in the critical path for the volume rendering module, as well as others
** Reformat widget to priority list? will require taking something out. Will is working on a new widget, wait on that. Andrey says the reformat widget will be useful in crop volume as well. General Slicer4 widget (was integrated in the 3d viewer in Slicer3). Nicole is taking on the integration of the vtk widgets.
* Contributing modules to Slicer4 (policy review)
** by default new modules should got to an external repository (NITRC, external module) and remain there for a while until whole module goes into Slicer4 if it's determined to be core functionality
** Slicer4 core to remail lean, but external modules to be first class citizens.
** Documentation requirements, building and testing on the factory machine every night.
** If a new module fails it shouldn't break Slicer4 building or running
** Timeline on extension mechanism in Slicer4?
*** Steve wanted to get the base nightly builds working first, but need to get the extensions built nightly asap
*** new feature in next release of cdash and cmake, ctest upload command to upload binaries, can get a list of uploads from dashboard
*** harvest the information from the cdash dashboard and make it available to the extension manager rather than have the extension manager communicate directly with the (sometimes slow) dashboards. Only let uploads come from factory machines. Use VMs to run test code.
*** Steve will be the gatekeeper to allow code to be built and tested on the factory for now
**** flag for if it gets redistributed, critical/non critical build
**** allow to build locally but submit to main slicer dashboard (no code upload), already supported via Experimental
** Greg: wants to be able to build a bug fixed version of an extension for an old release (limited support for it)

==2011-02-10==

Attendees: Jim, Mark, Tina, Nicole, Dan

Agenda:
*Updates from ITK meeting
*http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
**Heads up given to everyone that progress report is due on wiki by mid April

==2011-02-03==
Attendees: Suares, Dominik, Kilian, Dominique, Nicole, Daniel, Stephen, Tina, Xiaodong

Agenda:
*ITK meeting in progress in Boston. Steve and Jim attending it.
*http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0
**Automatic documentation generation options are being explored at Kitware. Stephen will report as progress is made.
*http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
**Heads up given to everyone that progress report is due on wiki by mid April

==2011-01-27==

No tcon today.

==2011-01-20==

Attendees: Xiaodong, Wendy, Tina, Mark, Nicole, Dominik, Daniel,

Agenda

* [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues Slicer 3.6.3]
* http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week
* http://wiki.na-mic.org/Wiki/index.php/Resources#Active_Job_Openings

==2011-01-06==

Attendees: Steve, Stephen, Jim, Ron, Tina, Dan Marcus, Xiaodong

Agenda:

*News: DCMTK 3.6 was released today
* http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week#Projects
* Command line module logic, supporting multiple argument for images in Slicer3/4
* Discussion of ITK support for large (greater than 4Gig) image volumes on win64. This will be further investigated at project week. It is only one of several issues to be researched as part of porting slicer3 and slicer4 to win64. Dave Partyka has a [[2011_Winter_Project_Week:64bit_Windows_Builds|project to work on this]] at project week.

File:Anonymized factorsExternalIDs with blage mriDate scanID daysSince.xlsx

2011-09-07T21:24:49Z

Mscully: uploaded a new version of "File:Anonymized factorsExternalIDs with blage mriDate scanID daysSince.xlsx"

Anonymized clinical factors for HD dataset

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-09-07T21:08:43Z

Mscully: Added data files

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:NAMIC_HD_Xnat_Interface.png|Screenshot of xnat interface for NAMIC_HD project
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UIowa: Hans Johson, Mark Scully

==Data Files==
*[[File:Anonymized_factorsExternalIDs_with_blage_mriDate_scanID_daysSince.xlsx]]
*[[File:NAMIC%2BFactors.doc]]

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

<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

</div>

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

<h3>Approach, Plan</h3>
Data will be made available via xnat.

</div>

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

<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.

Fill out the form [[File:NAMIC_DATA_SHARING.doc]] to request access.

After access has been granted and an account has been created you can fetch the raw data using the script [[File:Fetch_NAMIC_HD_data.sh.gz]] and the processed data using [[File:Fetch_NAMIC_HD_derived_data.sh.gz]].

The raw data is large (over 1TB) so it will take a long time and require a large amount of space.

Run either script with '-h' for terse help. Each file takes a basePath under which the output will be constructed of the form $basePath/NAMIC_HD/subjectID/scanID.zip for the raw data and $basePath/NAMIC_HD/subjectID/scanID_type.zip for the processed data. The raw data zip files expand to scanID/scans/scanTypes/resources/DICOM/files/ and the processed zip files expand to scanID/reconstructions/scanID_10_AUTO.NN3Tv20110419-BRAINSAutoWorkup/out/resources/resourceType/files/. When fetching the raw data you can specify a list of image types you are interested in using '-t' followed by a comma delimited list of scan types (It defaults to 'ALL'). You can get a list of possible scan types by running "./Fetch_NAMIC_HD_DATA.sh -l". The types you are likely to be interested in are at the beginning of the list. If either script is interrupted while running it can be restarted and it will skip over already downloaded zip files (provided you have not set force=True or deleted the relevant .zip files). If you run either command without a required input you will be prompted to provide it. Brief usage examples for each command follows:

usage: ./fetch_NAMIC_HD_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-l (list) List scan types and exit.<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>
-t scanTypes: comma delimited list of scan types. (Defaults to ALL) Ex: T1-30,T2-30<br>

usage: ./fetch_NAMIC_HD_derived_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>

</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat

File:NAMIC+Factors.doc

2011-09-07T21:07:57Z

Mscully: Explanation of anonymous clinical factors for HD data.

Explanation of anonymous clinical factors for HD data.

File:Anonymized factorsExternalIDs with blage mriDate scanID daysSince.xlsx

2011-09-07T21:06:25Z

Mscully: Anonymized clinical factors for HD dataset

Anonymized clinical factors for HD dataset

DBP3:Iowa

2011-09-01T20:29:36Z

Mscully: /* In Progress / Completed (Reverse Chronological) */

Engineering Action Plan

=== Overview of the project ===
http://www.na-mic.org/pages/DBP:HD

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Fall 2011) DTI noise estimation, Rician noise filtering
* (In Progress: Fall 2011) DTI pairwise registration (new Slicer module)
* (In Progress: Fall 2011) SPHARM-PDM Slicer3 integration/dissemination
* (In Progress: Fall 2011) Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
* (Complete: Summer 2011) DTI estimation, property map generation
* (Complete: Summer 2011) DTIPrep improvement
* (Complete: Spring 2011) Write Tutorial for DTIPrep
* (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** (Hans Johnson) Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team):
** Word doc Tutorial updated with visual inspection info
** Create Media Wiki version of documentation
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-05-01 (Revised: 2011-10-01) (Clement/Mahshid): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTIprep
* 2011-06-24 (Clement/Mahshid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation. Use of XML, extended reporting.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark/Mahshid): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Revised: 2011-10-15) (Clement): DTI pairwise registration (new Slicer module)
** Develop pairwise registration module allowing:
*** Scalar feature (e.g FA) to drive the registration of a DTI image
*** Direct registration of the DTI image (DTITK?)
** Investigate if both scalars and higher models can both be supported.
** Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite, alternative would be open source AtlasWorks
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for batch processing a large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools
** SPHARM shape summary tool
** Statistical Shape Analysis Tools
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

DBP3:Iowa

2011-09-01T20:23:25Z

Mscully: /* In Progress / Completed (Reverse Chronological) */

Engineering Action Plan

=== Overview of the project ===
http://www.na-mic.org/pages/DBP:HD

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Spring 2011) SPHARM-PDM Slicer3 integration/dissemination
* (In Progress: Spring 2011) Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
* (Complete: Summer 2011) DTIPrep improvement
* (Complete: Spring 2011) Write Tutorial for DTIPrep
* (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** (Hans Johnson) Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team):
** Word doc Tutorial updated with visual inspection info
** Create Media Wiki version of documentation
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-05-01 (Revised: 2011-10-01) (Clement/Mahshid): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTIprep
* 2011-06-24 (Clement/Mahshid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation. Use of XML, extended reporting.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark/Mahshid): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Revised: 2011-10-15) (Clement): DTI pairwise registration (new Slicer module)
** Develop pairwise registration module allowing:
*** Scalar feature (e.g FA) to drive the registration of a DTI image
*** Direct registration of the DTI image (DTITK?)
** Investigate if both scalars and higher models can both be supported.
** Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite, alternative would be open source AtlasWorks
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for batch processing a large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools
** SPHARM shape summary tool
** Statistical Shape Analysis Tools
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

DBP3:Iowa

2011-09-01T20:18:24Z

Mscully: /* DTI Processing */

Engineering Action Plan

=== Overview of the project ===
http://www.na-mic.org/pages/DBP:HD

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Spring 2011) SPHARM-PDM Slicer3 integration/dissemination
* (In Progress: Spring 2011) DTIPrep improvement
* (In Progress: Spring 2011) Write Tutorial for DTIPrep
* (In Progress: Spring 2011) Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
* (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** (Hans Johnson) Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team):
** Word doc Tutorial updated with visual inspection info
** Create Media Wiki version of documentation
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-05-01 (Revised: 2011-10-01) (Clement/Mahshid): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTIprep
* 2011-06-24 (Clement/Mahshid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation. Use of XML, extended reporting.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark/Mahshid): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Revised: 2011-10-15) (Clement): DTI pairwise registration (new Slicer module)
** Develop pairwise registration module allowing:
*** Scalar feature (e.g FA) to drive the registration of a DTI image
*** Direct registration of the DTI image (DTITK?)
** Investigate if both scalars and higher models can both be supported.
** Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite, alternative would be open source AtlasWorks
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for batch processing a large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools
** SPHARM shape summary tool
** Statistical Shape Analysis Tools
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

DBP3:Iowa

2011-09-01T20:12:06Z

Mscully: /* DTI Processing */

Engineering Action Plan

=== Overview of the project ===
http://www.na-mic.org/pages/DBP:HD

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Spring 2011) SPHARM-PDM Slicer3 integration/dissemination
* (In Progress: Spring 2011) DTIPrep improvement
* (In Progress: Spring 2011) Write Tutorial for DTIPrep
* (In Progress: Spring 2011) Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
* (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** (Hans Johnson) Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team):
** Word doc Tutorial updated with visual inspection info
** Create Media Wiki version of documentation
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-05-01 (Revised: 2011-11-01) (Clement/Mahshid): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTIprep
* 2011-06-24 (Clement/Mahshid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation. Use of XML, extended reporting.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark/Mahshid): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Clement): DTI pairwise registration (new Slicer module)
** Develop pairwise registration module allowing:
*** Scalar feature (e.g FA) to drive the registration of a DTI image
*** Direct registration of the DTI image (DTITK?)
** Investigate if both scalars and higher models can both be supported.
** Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite, alternative would be open source AtlasWorks
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for batch processing a large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools
** SPHARM shape summary tool
** Statistical Shape Analysis Tools
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

File:Fetch NAMIC HD data.sh.gz

2011-07-25T14:43:06Z

Mscully: uploaded a new version of "File:Fetch NAMIC HD data.sh.gz"

bash script to download the NAMIC_HD data from https://predict-hd.net/xnat. Depends on curl.

File:Fetch NAMIC HD derived data.sh.gz

2011-07-25T14:42:42Z

Mscully: uploaded a new version of "File:Fetch NAMIC HD derived data.sh.gz"

Script to download the processed data from the NAMIC_HD xnat project from UIowa.

2011 Summer Project Week Dicom2Nrrd

2011-06-24T15:50:18Z

Mscully: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:Dicom2NrrdUIPanel.png|UI Panel
</gallery>

'''Dicom To NRRD Converter'''

==Key Investigators==
* GE Research: Xiaodong Tao
* UIowa: Mark Scully

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

<h3>Objective</h3>


*Refactoring the DWI DicomToNrrdConverter using GDCM 2.x.

By separating the big (and only) .cxx file into multiple small classes that handle one type of data each, the maintainability of the entire code will be greatly improved. And the program can easily be extended into new vendor's format and new data types (for example, time series).

</div>

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

<h3>Approach, Plan</h3>


*Separate code for supporting different DICOM format from various vendors into individual classes.
*As a project week activity, we will code up the base class and implementation for one vendor format.
*The interface visible to the users (the driver program) will be keep unchanged.
</div>

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

<h3>Progress</h3>
* A large testing suite has been made available on MIDAS and committed to the Slicer3 version. It will be used for regression testing as the new version is developed.
* A stand alone new version using GDCM2 has been created.

</div>
</div>

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

==References==

*[[http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:DicomToNrrdRefactoring 2011 winter Utah project week]]
*[[NAMIC_Wiki:DTI:Nrrd_format | DTI:Nrrd_Format]]
*[[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI|DICOM_for_DWI_and_DTI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a command line module.

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-06-24T14:07:54Z

Mscully:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:NAMIC_HD_Xnat_Interface.png|Screenshot of xnat interface for NAMIC_HD project
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UIowa: Hans Johson, Mark Scully

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

<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

</div>

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

<h3>Approach, Plan</h3>
Data will be made available via xnat.

</div>

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

<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.

Fill out the form [[File:NAMIC_DATA_SHARING.doc]] to request access.

After access has been granted and an account has been created you can fetch the raw data using the script [[File:Fetch_NAMIC_HD_data.sh.gz]] and the processed data using [[File:Fetch_NAMIC_HD_derived_data.sh.gz]].

The raw data is large (over 1TB) so it will take a long time and require a large amount of space.

Run either script with '-h' for terse help. Each file takes a basePath under which the output will be constructed of the form $basePath/NAMIC_HD/subjectID/scanID.zip for the raw data and $basePath/NAMIC_HD/subjectID/scanID_type.zip for the processed data. The raw data zip files expand to scanID/scans/scanTypes/resources/DICOM/files/ and the processed zip files expand to scanID/reconstructions/scanID_10_AUTO.NN3Tv20110419-BRAINSAutoWorkup/out/resources/resourceType/files/. When fetching the raw data you can specify a list of image types you are interested in using '-t' followed by a comma delimited list of scan types (It defaults to 'ALL'). You can get a list of possible scan types by running "./Fetch_NAMIC_HD_DATA.sh -l". The types you are likely to be interested in are at the beginning of the list. If either script is interrupted while running it can be restarted and it will skip over already downloaded zip files (provided you have not set force=True or deleted the relevant .zip files). If you run either command without a required input you will be prompted to provide it. Brief usage examples for each command follows:

usage: ./fetch_NAMIC_HD_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-l (list) List scan types and exit.<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>
-t scanTypes: comma delimited list of scan types. (Defaults to ALL) Ex: T1-30,T2-30<br>

usage: ./fetch_NAMIC_HD_derived_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>

</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat

File:NAMIC HD Xnat Interface.png

2011-06-24T14:05:38Z

Mscully: Screenshot of xnat interface for NAMIC_HD project.

Screenshot of xnat interface for NAMIC_HD project.

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-06-23T22:24:29Z

Mscully: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UIowa: Hans Johson, Mark Scully

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

<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

</div>

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

<h3>Approach, Plan</h3>
Data will be made available via xnat.

</div>

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

<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.

Fill out the form [[File:NAMIC_DATA_SHARING.doc]] to request access.

After access has been granted and an account has been created you can fetch the raw data using the script [[File:Fetch_NAMIC_HD_data.sh.gz]] and the processed data using [[File:Fetch_NAMIC_HD_derived_data.sh.gz]].

The raw data is large (over 1TB) so it will take a long time and require a large amount of space.

Run either script with '-h' for terse help. Each file takes a basePath under which the output will be constructed of the form $basePath/NAMIC_HD/subjectID/scanID.zip for the raw data and $basePath/NAMIC_HD/subjectID/scanID_type.zip for the processed data. The raw data zip files expand to scanID/scans/scanTypes/resources/DICOM/files/ and the processed zip files expand to scanID/reconstructions/scanID_10_AUTO.NN3Tv20110419-BRAINSAutoWorkup/out/resources/resourceType/files/. When fetching the raw data you can specify a list of image types you are interested in using '-t' followed by a comma delimited list of scan types (It defaults to 'ALL'). You can get a list of possible scan types by running "./Fetch_NAMIC_HD_DATA.sh -l". The types you are likely to be interested in are at the beginning of the list. If either script is interrupted while running it can be restarted and it will skip over already downloaded zip files (provided you have not set force=True or deleted the relevant .zip files). If you run either command without a required input you will be prompted to provide it. Brief usage examples for each command follows:

usage: ./fetch_NAMIC_HD_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-l (list) List scan types and exit.<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>
-t scanTypes: comma delimited list of scan types. (Defaults to ALL) Ex: T1-30,T2-30<br>

usage: ./fetch_NAMIC_HD_derived_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>

</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat

File:Fetch NAMIC HD data.sh.gz

2011-06-23T22:24:20Z

Mscully: uploaded a new version of "File:Fetch NAMIC HD data.sh.gz"

bash script to download the NAMIC_HD data from https://predict-hd.net/xnat. Depends on curl.

File:Fetch NAMIC HD derived data.sh.gz

2011-06-23T22:23:30Z

Mscully: uploaded a new version of "File:Fetch NAMIC HD derived data.sh.gz"

Script to download the processed data from the NAMIC_HD xnat project from UIowa.

File:Fetch NAMIC HD derived data.sh.gz

2011-06-23T22:01:03Z

Mscully: uploaded a new version of "File:Fetch NAMIC HD derived data.sh.gz"

Script to download the processed data from the NAMIC_HD xnat project from UIowa.

File:Fetch NAMIC HD derived data.sh.gz

2011-06-23T21:58:39Z

Mscully: uploaded a new version of "File:Fetch NAMIC HD derived data.sh.gz"

Script to download the processed data from the NAMIC_HD xnat project from UIowa.

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-06-23T21:53:33Z

Mscully: /* Key Investigators */

File:Fetch NAMIC HD derived data.sh.gz

2011-06-23T21:53:20Z

Mscully: Script to download the processed data from the NAMIC_HD xnat project from UIowa.

Script to download the processed data from the NAMIC_HD xnat project from UIowa.

File:Fetch NAMIC HD data.sh.gz

2011-06-22T17:36:09Z

Mscully: uploaded a new version of "File:Fetch NAMIC HD data.sh.gz"

bash script to download the NAMIC_HD data from https://predict-hd.net/xnat. Depends on curl.

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-06-22T16:10:19Z

Mscully: /* Key Investigators */

File:Fetch NAMIC HD data.sh.gz

2011-06-22T16:08:00Z

Mscully: bash script to download the NAMIC_HD data from https://predict-hd.net/xnat. Depends on curl.

bash script to download the NAMIC_HD data from https://predict-hd.net/xnat. Depends on curl.

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-06-21T02:05:48Z

Mscully: /* Key Investigators */

File:NAMIC DATA SHARING.doc

2011-06-21T02:05:15Z

Mscully:

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-06-20T21:26:17Z

Mscully: /* Key Investigators */

2011 Summer Project Week Iowa Huntington's disease data sharing

2011-06-20T21:25:44Z

Mscully: Created page with '__NOTOC__ <gallery> Image:PW-MIT2011.png|Projects List </gallery> '''Full Title of Project''' ==Key Investigators== * Harvard Medical Scho…'

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

'''Full Title of Project'''

==Key Investigators==
* Harvard Medical School: Mohsen Mahvash

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

<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

</div>

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

<h3>Approach, Plan</h3>
Data will be made available via xnat.

</div>

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

<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.
Fill out the form [[file:notyet.doc]] to request access.

</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat

2011 Summer Project Week

2011-06-20T21:16:54Z

Mscully: /* Projects */ Added Iowa huntingtons data sharing project

Back to [[Events]]

[[image:PW-MIT2011.png|right|204px]]

[[image:Panorama-summer-2011.png|left|thumb|200px|[http://360.io/Afjepd Interactive Panorama of Project Week] (Works on chrome, maybe not on other browsers)]]
[[image:Pano2summer2011namic.jpg|left|thumb|200px|[http://botview.appspot.com/viewer/pan0.swf?panoSrc=/media/4104002&FOV=52 Interactive Panorama of Project Week] (Works on chrome, maybe not on other browsers)]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT ([http://whereis.mit.edu/?go=34 Grier Rooms Location on MIT Campus Map])

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:15pm''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Slides]]). <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>---<br>
'''4:15-5:00pm''' How to get DBP Data <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Right)]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

'''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''

#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Micah Chambers, Marcel Prastawa, Guido Gerig)
#[[Multimodality Image Registration for TBI]] (Yifei Lou, Danielle Pace, Jack Van Horn, Micah Chambers)
#[[2011_Summer_Project_Week_White_Matter_Laterality|White Matter Laterality in Python/Slicer4]] (Lauren O'Donnell)
#[[2011_Summer_Project_Week_Intraoperative_Brain_Shift_Monitor|Intraoperative Brain Shift Monitor]] (Jason White, Alex Golby, Steve Pieper, Junichi Tokuda)
#[[2011_Summer_Project_Week_GBM_Masks|Obtaining and Evaluation of Glioblastoma Multiforme (GBM) Segmentation Masks]] (Jan Egger,Tina Kapur, Andriy Fedorov, Rivka Colen, Ron Kikinis, Alex Golby, Christopher Nimsky)
#[[2011_Summer_Project_Week_NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#[[2011_Summer_Project_Week_Quantitative_Magnetic_Susceptibility_Mapping|Quantitative Magnetic Susceptibility Mapping ]] (Clare Poynton)

'''Radiation Therapy'''
#[[2011_Summer Project Week_Non-rigid_inter-patient_registration_of_bone_masks_derived_from_CT_for_Head_and_Neck_Cancer_Radiation_Therapy|Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy]] (Ivan Kolesov, Yi Gao, Gregory Sharp,Xiaodong Tao,Nadya Shusharina, Jan Egger, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_Contouring_Gyne_Structures|Contouring of Anatomy Structures like Tumor, Bladder, Rectum and Sigmoid for Gynecological Brachytherapy]] (Tina Kapur, Akila Viswanathan, Jan Egger)
#[[2011_Summer_Project_Week_Slicer_DICOM_RT_Brachytherapy|Visualization of DICOM RT Planning Contours and Dose Distributions for Prostate and Gynecologic Brachytherapy in Slicer]] (Firdaus Janoos, Jan Egger, Greg Sharp, Andriy Fedorov, Tina Kapur)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)

'''Huntington's Disease'''
#[[2011_Summer_Project_Week_Iowa_Huntington's_disease_data_sharing | Iowa Huntington's Disease Data Sharing]] (Hans Johnson, Mark Scully)
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] (Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#[[2011_Summer_Project_Week_long_shape_regression|Longitudinal Shape Regression - Huntington's Disease]] (James Fishbaugh, Marcel Prastawa, Guido Gerig, Hans Johnson)
#[[2011_Summer_Project_Week_DTIPrep|DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation]] - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#[[2011_Summer_Project_Week_DTI_PairWise_Registration|DTI pair-wise registration module]] - Huntington's Disease (Clement Vachet, Joy Matsui, Mark Scully, Martin Styner)
#[[2011_Summer_Project_Week_DTI analysis_for_Huntington's_disease | DTI analysis for Huntington's disease]] (Gopal Veni, Ross Whitaker)

'''Atrial Fibrillation'''
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Steve Pieper, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)

'''Device Integration with Slicer and General Image Guided Therapy'''
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#[[2011_Summer_Project__Week_Live_Tracked_Ultrasound|Live Tracked Ultrasound with Slicer4 (Tamas Heffter)]]
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#[[2011_Summer_Project_Week_Needle_Detection_to_Control_Scanner_for_Prostate_Biopsy | Needle Detection to Control Scanner for Prostate Biopsy ]] (Atsushi Yamada, Loïc Cadour, Junichi Tokuda and Nobuhiko Hata)
#[[2011_Summer_Project_Week_Segementation_Reconstruction_Pericardial_Sac]] (Mohsen Mahvash, Noby Hata, Ron Kikinis)
#[[2011_Summer_Project_Week_4DUltrasound_HybridProbe_OsteoPlan|4D Ultrasound / Hybrid Probe / OsteoPlan]] (Laurent Chauvin, Noby Hata)
#[[2011_Summer_Project_Week_AMIGO|AMIGO]] (Mallika Winsor, Vivian He, Dan Kacher, Tina Kapur)
#[[2011_Summer_Project_Week_Patient_Mounted_Robot|Patient-mounted Robot Control using OpenIGTLink]] (Conor James Walsh, Maryam Shokri, Faye Wu)

'''General Segmentation'''
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#[[2011_Summer_Project_Week_EMSegmentation_in_3D_Slicer4|EM Segmentation in 3D Slicer 4]] (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp, Daniel Haehn)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)

'''General Registration'''
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin, Ipek Oguz, Martin Styner, Dominik Meier)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_SlidingOrganRegistrationFED|Integrate Fast Explicit Diffusion into Sliding Organ Registration module]] (Danielle Pace)
#[[2011_Summer_Project_Week_Image_Manifold_Learning_with_Spectral_Embedding_and_Laplacian_Eigenmaps|Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps]] (Ramesh Sridharan, Polina Golland)

'''General Diffusion Tractography'''
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parametrize fiber tracts for fiber statistics analysis]] (Yundi Shi, Clement Vachet, Benjamin Yvernault, Anuja Sharma, Martin Styner)
#[[2011_Summer_Project_Week_ODF_though_Fiber_Counting | ODF computation through fiber counting]] (Yinpeng Li, Ipek Oguz, Martin Styner)
#[[2011_Summer_Project_Week_Nifti_Support_for_Diffusion_Tensor_Images|Nifti Support for Diffusion Tensor Images]] (Demian)
#[[2011_Summer_Project_Week_Finishing_details_on_the_workflows_DICOM_full_brain_tractography_peritumoral|Finishing details on the workflows: DICOM->Full brain tractography / peritumoral]] (Demian)
#[[Summer_project_week_2011_Finsler_Streamlines|Adding streamlined tractography to the Finsler front propagation tractography toolkit]] (Antonio Tristán-Vega)
#[[2011_Summer_Project_Week_Slicer4_Tractography_Interaction_and_Display|Tractography Bundle/Cluster Interaction and Display in Slicer4]] (Lauren O'Donnell, Isaiah, Demian)
#[[2011_Summer_Project_Week_DTI_Volumetric_Tractography | DTI Volumetric Tractography]] (Steve Callahan, Mark Scully, Jim Miller)
#[[2011_Summer_Project_Week_DWI_Atlas | Slicer module for building an average population DWI Atlas]] (Ryan Eckbo, Sylvain Bouix)
#[[2011_Summer_Project_Week_DTI_Volumetric_Segmentation_for_Group_studies | DTI Volumetric Segmentation for Group studies]] (Gopal Veni, Ross Whitaker)

'''Vessels'''
#[[2011_Summer_Project_Week_SlicerVmtk4|The Vascular Modeling Toolkit in 3D Slicer 4]] (Daniel Haehn, Luca Antiga, Steve Pieper, Kilian Pohl, Ron Kikinis)
#[[2011_Summer_Project__Week_Stenosis_Detector|Stenosis Detector in 3D Slicer 4]] (Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)

'''Infrastructure'''
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#[[2011_Summer_Project_Week_Dicom2Nrrd|DicomToNrrdConverter refactoring]] ( Xiaodong Tao, Mark Scully)
#[[Summer_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions]] (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)
#[[2011_Summer_Project_Week_Internationalization_of_Slicer|Internationalization of Slicer]] (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Julien Finet, Yiming Ge, Ping Cao)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th 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 40-50 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 is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[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 16: 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. XNAT/MIDAS). 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-3-6/#dirlist Slicer-3-6 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].

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration (see Logistics for link)
# Peter Anderson, Retired
# Nicole Aucoin, Brigham and Women's Hospital
# Dominique Belhachemi, University of Pennsylvania
# Anthony Blumfiled, Radnostics
# Lucile Bompard, UNC NIRAL
# Sylvain Bouix, Brigham and Women's Hospital
# Francois Budin, UNC NIRAL
# Steve Callahan, University of Utah
# Joshua Cates, University of Utah
# Micah Chambers, Laboratory of NeuroImaging
# Laurent Chauvin, Brigham and Women's Hospital
# Rivka Colen, Brigham and Women's Hospital
# Nikos Chrisochoides, Old Dominion University
# Adrian Dalca, Massachusetts Institute of Technology
# Manasi Datar, University of Utah
# Colin Davey
# Ryan Eckbo, Brigham and Women's Hospital
# Jan Egger, University Hospital of Marburg
# Luping Fang, Zhejiang University of Technology, China
# Mahshid Farzinfar, University of North Carolina at Chapel Hill
# Andriy Fedorov, Brigham and Women's Hospital
# Jean-Christophe Fillion-Robin, Kitware, Inc.
# Julien Finet, Kitware, Inc.
# James Fishbaugh, University of Utah
# Yi Gao, Georgia Institute of Technology
# Greg Gardner, University of Utah
# Ronen Globinsky, Yale University
# Vivian He, Brigham and Women's Hospital
# Maged Goubran, Robarts Research Institute
# Daniel Haehn, University of Pennsylvania
# Mike Halle, Brigham and Women's Hospital
# Marcus Hanwell, Kitware, Inc.
# Firdaus Janoos, Brigham and Women's Hospital
# Noby Hata, Brigham and Women's Hospital
# Tamas Heffter, Queen's University
# Nicholas Herlambang, AZE, Ltd.
# Luis Ibanez, Kitware, Inc.
# Andrei Irimia, University of California, Los Angeles
# Hans Johnson, University of Iowa
# Ilknur Kabul, Kitware, Inc.
# Tina Kapur, Brigham and Women's Hospital
# Peter Karasev, Georgia Institute of Technology
# Ron Kikinis, Brigham and Women's Hospital
# Regina Kim, University of Iowa
# Ivan Kolesov, Georgia Institute of Technology
# Szymon Kostrzewski, Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee, University of Utah
# Yinpeng Li, UNC-NIRAL
# Yifei Lou, Georgia Institute of Technology
# Mohsen Mahvash, Harvard Medical School (BWH and VA)
# Nikos Makris, Massachusetts General Hospital
# Katie Mastrogiacomo, Brigham and Women's Hospital
# Joy Matsui, University of Iowa
# Dominik Meier, Brigham and Women's Hospital
# Mikhail Milchenko, Washington University in St. Louis
# James Miller, GE Research
# Zach Mullen, Kitware, Inc.
# Isaiah Norton, Brigham and Women's Hospital
# Lauren O'Donnell, Brigham and Women's Hospital
# Danielle Pace, Kitware, Inc.
# Beatriz Paniagua, University of North Carolina at Chapel Hill
# Xenophon Papademetris, Yale University
# Kedar Patwardhan, GE Global Research
# Steve Pieper, Isomics, Inc.
# Csaba Pinter, Queen's University
# Wendy Plesniak, Brigham and Women's Hospital
# Kilian Pohl, University of Pennsylvania
# Marcel Prastawa, University of Utah
# Sonia Pujol, Brigham and Women's Hospital
# Martin Rajchl, Robarts Research Institute
# Ramesh Sridharan, Massachusetts Institute of Technology
# Petter Risholm, Brigham and Women's Hospital
# Peter Savadjiev, Brigham and Women's Hospital
# Will Schroeder, Kitware, Inc.
# Andreas Schuh, University of Pennsylvania
# Mark Scully, University of Iowa
# Gregory Sharp, Massachusetts General Hospital
# Junichi Tokuda, Brigham and Women's Hospital
# Yundi Shi, University of North Carolina at Chapel Hill
# Matthew Toews, Brigham and Women's Hospital
# Nadya Shusharina, Massachusetts General Hospital
# Hao Su, Worcester Polytechnic Institute
# Suares Tamekue, Brigham and Women's Hospital
# Xiaodong Tao, GE Research
# Clement Vachet, UNC Chapel Hill
# Antonio Vega, Brigham and Women's Hospital
# Gopal Veni, University of Utah
# Bo Wang, University of Utah
# Andrew Wassam, CoSMo Software Inc.
# Demian Wassermann, Brigham and Women's Hospital
# Sandy Wells, Brigham and Women's Hospital
# Jason White, Brigham and Women's Hospital
# Mallika Winsor, Brigham and Women's Hospital
# Atsushi Yamada, Brigham and Women's Hospital
# Alexander Yarmarkovich, Isomics, Inc.
# Alexander Zaitsev, Brigham and Women's Hospital
# Ming Zhao, Sun Yat-Sen University Cancer Center, GuangZhou, China

2011 Summer Project Week Registration of mouse brains

2011-06-20T19:11:19Z

Mscully: /* Key Investigators */ Added BRAINSFit documentation link

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:notfound.png|Interesting picture to be added...
</gallery>

'''Registration of mouse brain'''

==Key Investigators==
* UNC NIRAL: Francois Budin, Ipek Oguz, Martin Styner
* BWH: Dominik Meier

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

<h3>Objective</h3>

Registration of mouse brain images is really hard to achieve properly with certain types of images (in particular T1).Indeed, the size of those images is very different from the size of human brain images. The ratio of rotation, translation and scaling in the transformations is going to be very different in both case. Most modules included in Slicer have default parameters set up for human images. The goal of this project is to provide a framework that is adapted to register easily and automatically mouse brain images in Slicer.

</div>

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

<h3>Approach, Plan</h3>

During the NAMIC project week, I will try to run the different registration modules available in Slicer to figure out some good sets of parameters that allow good mouse brain registrations. This results will be integrated in DWIProcessPipeline, a module for Slicer that will compute a DTI from a DWI image, register a scalar image computed from the DTI to a template and then computes scalar images from the registered DTI.
* Usecase #3 in the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit documentation] demonstrates mouse brain registration using BRAINSFit.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module

2011 Summer Project Week DTI PairWise Registration

2011-06-16T19:21:19Z

Mscully: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:notfound.png|Interesting picture to be added...
</gallery>

'''Full Title of Project'''

==Key Investigators==
* UNC: Clement Vachet, Martin Styner
* UIowa: Joy Matsui, Mark Scully

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

<h3>Objective</h3>

#:A Slicer module that will register two DWI images together.

</div>

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

<h3>Approach, Plan</h3>
#:Initial version will use scalar features (FA) to drive the registration between two DTI images. We will then investigate a method to perform pair-wise registration directly from DWI images.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==References==
D’Avila A, Scanavacca M, Sosa E, Riskin JN, Reddy VY. Pericardial anatomy for the Interventional Electrophysiologist. J Cardiovasc Electrophysiol 2003;14:422-430

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week DTI PairWise Registration

2011-06-16T19:16:35Z

Mscully: Saving example template

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:notfound.png|Interesting picture to be added...
</gallery>

'''Full Title of Project'''

==Key Investigators==
* Harvard Medical School: Mohsen Mahvash

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

<h3>Objective</h3>

#:Segmentaion and 3d
#:reconstruction of pericardial sac
#: (a thin tissue layer that covers the heart)

</div>

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

<h3>Approach, Plan</h3>
#:Trying 3dslicer modules
#:for segmentation
#:and 3d reconstruction

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
D’Avila A, Scanavacca M, Sosa E, Riskin JN, Reddy VY. Pericardial anatomy for the Interventional Electrophysiologist. J Cardiovasc Electrophysiol 2003;14:422-430

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week

2011-06-13T18:57:19Z

Mscully: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
#Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
#Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
#Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Mark Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
#Integrate BRAINSCut into Slicer3(Regina Kim, ... )
#The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
#Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Mark Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
#Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
#Refactoring of the tractography display widget (Isaiah)
#Laterality (Lauren)
#Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
#Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#Slicer module for building an average population HARDI Atlas (Ryan Eckbo)
#4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)
#EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Jean-Christophe, Julien Finet, Yiming Ge, Ping Cao)
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. 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. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th 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 40-50 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 is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[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 16: 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. XNAT/MIDAS). 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-3-6/#dirlist Slicer-3-6 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].

==Registrants==

Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)
#Bompard, Lucile- UNC NIRAL
#Belhachemi, Dominique- University of Pennsylvania
#Blumfiled, Anthony- Radnostics
#Budin, Francois- UNC NIRAL
#Callahan, Steve- University of Utah
#Cates, Joshua- University of Utah
#Datar, Manasi- University of Utah
#Davey, Colin-
#Farzinfar, Mahshid- UNC
#Finet, Julien- Kitware
#Fishbaugh, James- University of Utah
#Gardner, Greg- University of Utah
#Globinsky, Ronen- Yale University
#Goubran, Maged- Robarts Research Institute
#Haehn, Daniel- University of Pennsylvania
#Halle, Mike - BWH/HMS
#Heffter, Tamas- Queen's University
#Irimia, Andrei- University of California, Los Angeles
#Johnson, Hans- University of Iowa
#Kapur, Tina- Brigham and Women's Hospital; Harvard Medical School
#Kikinis, Ron- Brigham and Women's Hospital; Harvard Medical School
#Kim, Regina- University of Iowa
#Kostrzewski, Szymon- Ecole Polytechnique Federale de Lausanne EPFL
#Lee, Dillon- University of Utah
#Li, Yinpeng- UNC-NIRAL
#Lou, Yifei- Georgia Institute of Technology
#Mastrogiacomo, Katie- Brigham and Women's Hospital
#Matsui, Joy- University of Iowa
#Meier, Dominik- BWH
#Milchenko, Mikhail- Washington University in St. Louis
#Miller, James- GE Research
#Pace, Danielle- Kitware
#Paniagua, Beatriz- University of North Carolina at Chapel Hill
#Papademetris, Xenophon- Yale University
#Patwardhan, Kedar- GE Global Research
#Pieper, Steve- Isomics, Inc.
#Pinter, Csaba- Queen's University
#Pohl, Kilian- UPenn
#Prastawa, Marcel- University of Utah
#Rajchl, Martin- Robarts Research Institute
#Schuh, Andreas- University of Pennsylvania
#Scully, Mark- University of Iowa
#Sharp, Gregory- MGH
#Shi, Yundi- UNC Chapel Hill
#Vachet, Clement- UNC Chapel Hill
#Wang, Bo- University of Utah
#Wells, Sandy- BWH/HMS
#Yamada, Atsushi- Brigham and Women's Hospital
#Yarmarkovich, Alexander- Isomics

DBP3:Iowa

2011-04-27T16:28:08Z

Mscully: /* In Progress / Completed (Reverse Chronological) */

Engineering Action Plan

=== Overview of the project ===
http://www.na-mic.org/pages/DBP:HD

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Spring 2011) SPHARM-PDM Slicer3 integration/dissemination
* (In Progress: Spring 2011) DTIPrep improvement
* (In Progress: Spring 2011) Write Tutorial for DTIPrep
* (In Progress: Spring 2011) Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it. This has been worked around in BRAINS Tools by forcing MI registration metric to be single threaded until the ITK community can correct it.
* (Complete: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes. Identified data and we are actively working on creating the data set as of March 2011.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** (Hans Johnson) Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms. -- This is not as easy as expected, and it is probably not a good use of our time to make this more automated. It will continue to be done manually.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team):
** Word doc Tutorial updated with visual inspection info
** Create Media Wiki version of documentation
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** 2010-12-31 (Clement) DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-05-01 (Clement): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTIprep
* 2011-06-24 (Clement/Mashid): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation. Use of XML, extended reporting.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark/Mahshid): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Clement): DTI atlas registration (new Slicer module)
** Investigate if both scalars and higher models can both be supported.
** Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite, alternative would be open source AtlasWorks
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for
** Batch procesing for running large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools
** SPHARM shape summary tool
** Statistical Shape Analysis Tools
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2012-08-01 (Clement/Bea): Add support for particle shape analysis as part of shape pipeline
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet, Mahshid Farzinfar (DTIPrep), Beatriz Paniagua (Shape)
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

DBP3:Iowa

2011-03-11T21:05:48Z

Mscully: /* In Progress / Completed (Reverse Chronological) */

Engineering Action Plan

=== Overview of the project ===
http://www.na-mic.org/pages/DBP:HD

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Spring 2011) Write Tutorial for DTIPrep
* (In Progress: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes.
* (In Progress: Spring 2011) Identified a bug in Mattes mutual information metric related to multithreading the was affecting BRAINSFit. Working with the ITK community to correct it.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: March 2011) Fixed BRAINSTools errors on Windows
* (Complete: Feb 2011) Moved all BRAINS testing data to midas.kitware.com and updated the tests to pull data from there.
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team): Write Tutorial for DTIPrep
** Create Media Wiki version of documentation with screen shots describing how visual inspections are to occur.
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** Target 2010-12-31 (Clement): Document how to interpret B-Matrix for Siemens (extration from dicom) on the DicomToNrrd Wiki page
** Target 2010-12-31 (Clement) Investigate DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-03-01 (Clement): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTI-PREP
* 2011-06-24 (Clement): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Clement): DTI atlas registration (new Slicer module)
** Investigate if both scalars and higher models can both be supported.
** Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite with new greedy registration methods
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for
** Batch procesing for running large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools (exists, needs polishing)
** SPHARM shape summary tool (exists, needs polishing)
** Statistical Shape Analysis Tools (exists, needs polishing)
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2013-08-01 (Clement): Add support for particle shape analysis (new Slicer module)
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

DBP3:Iowa

2011-03-11T19:54:04Z

Mscully: /* In Progress / Completed (Reverse Chronological) */

Engineering Action Plan

=== Overview of the project ===
http://www.na-mic.org/pages/DBP:HD

=== In Progress / Completed (Reverse Chronological) ===

* (In Progress: Spring 2011) Write Tutorial for DTIPrep
* (In Progress: Spring 2011) Re-deidentify data subset and post to XNAT for NA-MIC purposes.
* (Complete: Spring 2011) Process data from raw DICOM data (enhanced DicomToNRRDConverter)
* (Complete: Feb 2011) Final approval from the Predict Steering Committee to share data.
* (Complete: Jan 2011) Add testing data suite to DicomToNRRDConverter
* (Complete: Fall 2010) Over 2900 scan sessions collected.

=== Morphometric Processing ===
Goals: Have all the documentation and code in place for BRAINS3 to easily be used by the community.
* 2011-02-15 (Mark Scully): Prepare the BRAINS3 Toolkit for public use
** Improve the consistency of the command line argument processing
*** Create an XML formal Schema from the SEM model examples
*** Enhance the SEM schema with other optional tags needed for improved documentation
*** Make SEM into it's own External_Add project to ease use by other packages
*** Move internal documentation from https://www.icts.uiowa.edu/confluence/display/BRAINS/Command+line+argument+rules, to the SEM pages section
** Improve merging strategies between BRAINS3Tools that are part of BRAINS3 and BRAINS3Tools that are part of Slicer3. A combination of git svn should ease the integration of these two platforms.
* 2012-01-15 (Mark Scully): Create documentation for a standard morphometric analysis
* 2013-01-08 (Mark Scully): Create tutorial for full morphometric analysis suitable for basing a DWI based analysis on.

=== DTI Processing ===
Goals: Tools for a longitudinal analysis pipeline of changes measured by fiber tractography to identify white matter tracts that have strong co-morbid degenerative timelines compared to subcortical degeneration over time. Enable the use of the advanced DTI processing in NA-MIC within PREDICT HD. Specifically, adapt all NA-MIC tools to work as individual external Slicer modules (in part they already exist, but need further work), as well as combine them into a single Slicer DTI processing wizard.
* 2010-12-15 (Mark, Joy, UNC Team): Write Tutorial for DTIPrep
** Create Media Wiki version of documentation with screen shots describing how visual inspections are to occur.
** Create PPT presentation for DTIPrep.
* Process data from raw DICOM data (enhanced DicomToNRRDConverter)
** 2010-11-30 (Mark, Joy): Add testing data suite to DicomToNRRDConverter (Joy to identify, Mark to implement)
** Target 2010-12-31(Mark): CMake URL data download mechanisms (Look at Titan CMake has examples of this).
** Target 2010-12-31 (Clement): Document how to interpret B-Matrix for Siemens (extration from dicom) on the DicomToNrrd Wiki page
** Target 2010-12-31 (Clement) Investigate DicomToNRRDConverter use of B-Matrix for vb13 data DTI_THP Iowa data.
* Target 2011-03-01 (Clement): DTI noise estimation, Rician noise filtering
** Review status of code to determine how to modularize into stand alone library and executable
** Include directly into DTI-PREP
* 2011-06-24 (Clement): DTI QC and motion/eddy current correction (enhanced DTIPrep)
** Reporting standardization for easier report generation.
** Loading reports so that batch processing mode and gui processing mode allow the same user
** GUI should allow for manual individual rejection of DWI gradients
* 2011-12-31 (Clement/Mark): DTI estimation, property map generation (existing Slicer modules)
** Review and make command line interfaces and make a dictionary of common command line arguments across the tool sets.
** Push DTIProcess tools into full Slicer Modules
* 2011-08-15 (Clement): DTI atlas registration (new Slicer module)
** Investigate if both scalars and higher models can both be supported.
** Investigate DTITK inclusion Slicer3
* 2012-05-01 (Clement): DTI atlas based fiber analysis (new Slicer module)
** Tools need re-writing to make them slicer3 compatible.
* 2012-07-01 (Clement): DTI atlas computation module (new Slicer module)
** NITRC implementation FRAT needs rewrite with new greedy registration methods
* 2012-09-01 (Clement): DWI atlas mapping tool (new Slicer module)
** Need to move to NITRC and convert to Slicer3
* 2013-01-01 (Clement/Mark/Jeff/All): Appropriate reporting of all steps
** Reporting of tool status. Track the OpenProvenance project.
** Use XML so that we can convert of OpenProvenance latter if desired.
* 2013-08-30 (Mark): DTI processing wizard in Slicer
* 2013-08-30 (Clement): Longitudinal DTI analysis module
** Create processing pipeline for
** Batch procesing for running large number of data sets
* 2013-08-30 (Steve Pieper/Kitware/Core 2 involvement): Fiber profile measurement/visualization within Slicer

=== Shape Analysis ===
Goals: Tools for a longitudinal shape analysis pipeline to identify localized changes in basal ganglia tracts that have strong co-morbid degenerative timelines. Enable the use of the advanced SPHARM & particle shape analysis processing in NA-MIC within PREDICT HD.
* 2011-04-01 (Slicer Team/Core2):Sun Grid Engine compatibility
* 2011-04-01 (Clement): Clean up existing tools for deployment at Iowa
** Individual SPHARM tools (exists, needs polishing)
** SPHARM shape summary tool (exists, needs polishing)
** Statistical Shape Analysis Tools (exists, needs polishing)
*** CSV files as part of Slicer standards (Paths, variables, group associations, etc)
* 2012-01-01 (Mark): Analyze 225 subjects with Cross sectional tools
** With between 3-6 longitudinally collected scans.
** With Caudate/Putamen/Thalamus
* 2013-08-01 (Clement): Add support for particle shape analysis (new Slicer module)
** Target of 2011-01-14: have feasibility shape analysis done to identify outstanding work that needs to be done.

=== BatchMake Processing and Grid Wizard ===
Goals: Create a distributed batch processing pipeline that pulls data from and reports data to XNAT while distributing jobs across a cluster.
* 2011-01-14 (Marco): Contact BatchMake developers and determine what needs to be done in order to distribute computational load for the analysis of this project.
** 2011-06-24 (Marco): Distribute from local data repositories.
** 2012-06-24 (Marco/Kevin Archie/Tim Olsen): Distribute from XNAT
** 2011-01-14 (Marco/Kevin Archie): Define mechanism for deploying distributed computations with GridWizard as a backend tool that the end-user never sees.

=== Data ===
Goals: Share a meaningful, fully anonymized subset of the sMRI, fMRI, and DWI Huntington's data.
* (Target date of 2010-12-10) Identified the FMRI_024 data (77 subjects, 2-3 years longitudinal) as a good candidate data set for collaborative algorithm development platform. This data set has 3 71direction+8B0 DTI data sets, 2 1.0^3 T1 data sets, and a 0.56x0.56x1.4 T2 data set.
** Will likely need to collect clinical data for shape analysis work that includes: (Age, Gender, Dx, Burdon Score, Motor Score).
** Will need to re-de-identify all the data to be used here.
** Will need to run auto-workup for generating Caudate/putamen/hippocampus/thalmus masks.
** Data exchange will be done through XNAT. including derived data.
* (Target date of 2011-01-14): Share all DTI_THP to wide NAMIC group for validation of tools being developed.

=== Outreach ===
Goals: Inform community of the existence of tools and data sets as well as train them on their use.
*Tutorial(s) on the wiki
*Presentations at HBM, Euro-HD.net, HDSA (The Huntington's Disease Society of America) in year 2
*Hands-on teaching event for the DBP scientific community for year 3

===Who===
*DBP: Hans Johnson, DBP engineer Mark Scully
*Algo: Martin Styner, DBP engineer Clement Vachet
*Eng: Dan Marcus, Jeff Grethe, Marco Ruiz

DBP2:MIND:Introduction

2011-01-18T17:17:09Z

Mscully: /* Team and Institute */

Back to [[DBP2:MIND|MIND DBP 2]]
__NOTOC__
=The Analysis of Brain Lesions in Neuropsychiatric Systemic Lupus Erythematosus =
==Team and Institute==
*Co-PI: H Jeremy Bockholt (jbockholt at themindinstitute.org)
**505 272 5682 desk (preferred)
**505 417 9071 mobile (alternative)
*Co-PI: Charles Gasparovic (chuck at unm.edu)
*Software Engineer: Mark Scully (mark-scully at uiowa.edu)
*NA-MIC Engineering Contact: Steve Pieper, Isomics
*NA-MIC Algorithms Contact: Ross Whitaker, Utah
*Host Institues: [http://www.themindinstitute.org The MIND Institute] and [http://www.unm.edu The University of New Mexico]

==Research Goals==
Systemic lupus erythematosus (SLE) is an autoimmune disease affecting multiple tissues, including the brain. Estimates of SLE prevalence range from 14.6-372 per 105 (1). Neuropsychiatric SLE (NPSLE), a term that subsumes the neurologic and psychiatric complications of SLE, occurs in up to 95% of SLE patients (2). While MRI often reveals distinct white matter abnormalities in active NPSLE, the pathologic processes underlying these lesions, whether purely autoimmune or vascular (e.g., hemostasis), are unknown.

Currently we are testing hypotheses concerning the possible thrombotic or embolic origin of white matter brain lesions in NPSLE and, ultimately, the cause of cognitive dysfunction in NPSLE. Specifically, we are examining whether the incidence of lesions correlates with either levels of thrombosis markers or emboli in the blood or a potential source of emboli in the heart. We will also examine whether overall lesion load or the levels of particular classes of lesion correlate with cognitive function. Diffusion-weighted, T1-weighted, and T2-weighted MRI are used to classify normal tissue and lesions. Additionally, blood flow is measured with perfusion-weighted imaging and vascular status is assessed with MR angiography.

Critical to understanding the etiology of brain lesions in NPSLE will be the accurate measurement of their location, size, and time course. Lupus brain lesions are known to vary in MRI intensity and temporal evolution and include acute, chronic, and resolving cases. Monitoring the time course of image intensity changes in the vicinity of lesions, therefore, may serve to classify them based on their temporal characteristics. Hence, a major objective of this DBP will be the evaluation of existing tools and the development new tools within SLICER for the time series analysis of brain lesions in lupus.

Grant # R01HL077422, PI: ROLDAN, CARLOS A.

==Data==

The MRI data in this project are collected on a 1.5T Siemens Sonata scanner using an 8-channel head coil. Whole-brain images to measure brain volume changes and identify lesions are obtained with three co-registered pulse sequences in an oblique-axial plane aligned with the interhemispheric midline and parallel to the anterior commissure-posterior commissure (AC-PC) line:
# a T1-weighted 3D fast low angle shot (FLASH) sequence (TR/TE = 12/4.76ms, flip angle = 20deg, FOV = 220x220mm, resolution = 192x192, 120 1.5-mm slices, total time = 6m32s),
# a T2-weighted fast spin echo sequence (TR/TE = 9040/64ms, turbofactor=5, FOV = 220x220mm, resolution = 192x192, 120 1.5-mm slices, total time = 6m2s)
# a Fluid Attenuated Inversion Recovery (FLAIR)/fast spin echo sequence (TR/TE = 1000/105ms, TI = 2500ms, echo train=9, field of view (FOV) = 220x220mm, resolution = 192x192, 88 1.5-mm slices, total time = 9m2s).

We employ a perfusion-weighted EPI sequence to follow the first pass of a contrast bolus through the brain (TR/TE = 2120ms/65ms, flip angle = 90º, 20 5-mm slices, a time course of 60 sequential acquisitions, FOV=220x220 mm, matrix size 128x128). From the signal intensity curve calculated over the time series, relative cerebral blood flow, relative cerebral blood volume, and relative mean transit time are calculated. MR angiography is performed with a region of interest centered on the circle of Willis using a 3D FLASH-based time-of-flight sequence (TR/TE = 40ms/7.15ms, flip angle = 25º, FOV=200x200 mm, matrix size 256x256, 128 0.8-mm slices, scan time=6m27s)

In addition to MRI, transcranial doppler ultrasound is used to detect microemboli in the brain and transesophageal echocardiography is performed to evaluate general cardiac status and to detect the presence of heart valve vegetations, as potential sources of emboli. A number of laboratory tests on blood samples are performed to detect markers of hemostasis, including analyses for platelets, coagulation, fibrinolysis, and anti-phospholipid antibodies. Finally, a battery of neuropsychological tests is administered to evaluate cognitive function. These exams, along with the MRI, will be performed on approximately 60 SLE patients and 30 normal control subjects over a period of 48 months. A subset of this group will be approximately 15 SLE subjects with NPSLE and 15 SLE subjects without NSLE who are recruited and examined during the first year of the study. A subset of these initial SLE groups will be re-examined in the each of the subsequent years (2-4) of the study.

==Image Processing Needs==
Our major image processing needs in this project revolve around lesion segmentation and time series analysis. Hence, we need a robust and reliable method capable of segmenting the brain into at least four classes: gray matter, white matter, cerebrospinal fluid, and white matter lesions. Furthermore, in order to follow changes in lesions with time, and to allow the possibility of sub-classifying lesions according to their temporal features, we will need methods of normalizing and registering images obtained in different scanning sessions. Ultimately, such tools will allow us to ask questions such as whether the appearance of and changes in particular lesions correlate with the onset and remission of the neuro-psychiatric symptoms of NPSLE.

A goal of the project will be to make this analysis fully automated. The input data will be image data from the T1-weighted, T2-weighted, and FLAIR sequences described above. Output data will be probability maps for each tissue class, the number of lesions, the volume of each lesion, and the total lesion volume at each time point. Additionally, changes in lesion size and changes in pixel intensity within the volume of each lesion will be displayed graphically. The time course data will also be amenable to time series analysis by statistical tools such as general linear modeling (GLM), independent component analysis (ICA), and Bayesian analysis.

==Current Image Processing Tools==
Presently at the MIND Institute, a number of different MRI data analysis tools are used by researchers. These include modules in BRAINS2, FSL, SPM, Freesurfer, and Slicer for image segmentation and labeling and FSL, SPM, and AFNI for fMRI data analysis. The tissue classifying modules in these tools where developed for the segmentation of normal appearing tissue and none - except perhaps for Slicer recently - has been shown to be useful for lesion analysis. While other software tools are commercially available for lesion analysis of image data (e.g., Analyze), they are generally expensive and cross-validation studies on their performance are lacking.

==What We Will Do with the NA-MIC Kit==
We will implement a novel best practice automated lesion segmentation algorithm that takes advantage of the strengths of existing algorithms and is implemented using the ITK framework. We will develop a module for Slicer that quantifies various lesion parameters and performs time series analyses on these parameters. A software engineer will be hired to implement these modules within Slicer, supervised jointly by Chuck Gasparovic and H. Jeremy Bockholt at the MIND Instutute. Vincent Magnotta, a tissue segmentation expert at the University of Iowa, and Wilber Sibbitt, the co-PI of the NPSLE project will act as consultants on the project.

More specifically, this project will proceed in three phases:

# We will evaluate the performance of at least four methods for lesion segmentation on a set of brain images:
## a method using Slicer, developed by Sandy Wells,
## a modification of this method involving pre-processing steps, developed by Vincent Magnotta,
## a method using BRAINS2, and
## manual classification by an expert rater. If warranted, other algorithms will be evaluated. We will use the STAPLE and/or a method using the Williams Index to cross-validate these methods.
# We will implement within Slicer methods for the registration and normalization of MRI images obtained in different scanning sessions, allowing the time series analysis of the data on a pixel-by-pixel basis.
# We will experiment with different statistical methods of time series analysis of these data, drawing from methods that have been successful in the analysis of fMRI data, including GLM and ICA. For example, we will experiment with the use of GLM or multiple regression analysis to examine correlations between changes in lesion intensity or size and measures of thrombo-embolic activity or the onset of clinical symptoms of NPSLE, as described above. If any of these methods proves useful in the analysis of the NPSLE data set, we will consider applying for external funds to implement them within the Slicer framework in a future project.

==Direction that this DBP Will Drive NA-MIC==
The successful implementation of the methods developed in this DBP will have a broad impact on the study of brain diseases involving MRI-visible lesions. The origin of these lesions in many diseases - including NPSLE, vascular dementia, and multiple sclerosis - is still unknown. Moreover, it is not clear in many cases whether there are multiple causes for lesions, even within one subject (e.g., both autoimmune and embolic). The accurate characterization of the time evolution of these lesions, therefore, will undoubtedly help to elucidate not only the origins of the lesions but their relationships to disease symptoms. No image analysis software package currently permits this level of lesion analysis. Hence, the availability of these tools within Slicer will give it a unique position among software for brain lesion analysis.

==Summary==
We will augment, develop, and validate tools within Slicer for the quantification of brain lesions thought to underlie the cognitive dysfunction of NPSLE. Furthermore, we will develop tools to analyze changes in these lesions with time and to relate these changes to the fluctuating symptoms of NPSLE. Our primary goal in the work, of course, is to gain greater insight into the causes of NPSLE. However, if successful, we will apply these tools to other brain diseases currently under investigation at UNM and The MIND Institute, including vascular dementia, myotonic dystrophy, and multiple sclerosis.

==References==
# Aladjem, H (Editor): LFA study shows between 1,400,000 and 2,000,000 people diagnosed with lupus. Lupus News 14:12, 1994.
# Sibbitt WL Jr, Brandt JR, Johnson CR, Maldonado ME, Patel SR, Ford CC, Bankhurst, AD, BrooksWM: The incidence and prevalence of neuropsychiatric syndromes in pediatric-onset systemic lupus erythematosus. J Rheum 2002 29:1536-42.
# Warfield SK, Zou KH, Wells WM. Simultaneous truth and performance level estimation (STAPLE): an algorithm for the validation of image segmentation. IEEE Trans Med Imaging. 2004 Jul;23(7):903-21.
# Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME. Two methods for validating brain tissue classifiers. Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):515-22.

==Presentations==
*[http://www.na-mic.org/Wiki/index.php/AHM2010:Mind 2010 AHM Presentation]
*[http://www.na-mic.org/Wiki/index.php/AHM2009:Mind 2009 AHM Presentation]
*[[Media:Lupus-dbp-summary-final.ppt | 2007 AHM Presentation]]

==Projects==

*Roadmap [[DBP2:MIND:Roadmap]]
*2010 Winter Project Week
**[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]]
**[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]]
**[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]]
*2009 Summer Project Week: [[2009_Summer_Project_Week_Lupus_Lesion_Segmentation|Lupus Lesion Segmentation]]
*2009 Winter Project Week: [[DBP2:MIND:Roadmap|MIND Roadmap Project: Brain Lesion Analysis in Lupus]]
**[[2009_Winter_Project_Week:HighLevelWizard|Slicer High Level Wizard Project]]
**[[2009_Winter_Project_Week:LesionAlgorithms|Review of Lesion Algorithms]]
**[[2009_Winter_Project_Week:LongitudinalLesions|Determine Requirements of Longitudinal Lesion Analyses]]
**[[2009_Winter_Project_Week:LesionSegmentationEfficiency|Optimize the new segmentation method for speed, memory use, and multi-threading]]
*2008 Summer Project Week: [[DBP2:MIND|Analysis of Brain Lesions in Lupus]]
**[[DBP2:MIND:RoadmapProject|Lesion Classification Module]]
**[[DBP2:MIND:LongitudinalRegistrationProject|Longitudinal Registration and time course analyses in white matter lesions]]
**[[DBP2:MIND:BeyondLesionsProject|Enhancements and extension of white matter lesion classification using DTI scalars]]
*2008 Winter Project Week: [[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]]
*2007 Summer Project Week: [[Projects/Structural/2007_Project_Week_Lesion_Classification_in_Lupus|Lesion Classification in Lupus]]

Data:DBP2:MIND

2011-01-18T17:14:38Z

Mscully: /* Data Contact */

Back to [[DBP2:MIND|MIND DBP 2]], [[Data:DBP2|DBP 2 Data]]
__NOTOC__
== MIND Data ==

=== Data Access ===
[[Media:20081114_public_lupus_data_tutorial_release.tgz|5 Lupus White Matter Lesion Datasets]]

=== Data Description ===

5 Lupus Patient Datasets.
co-registered
T1-weighted
T2-weighted
FLAIR
masks for brain and lesions

Entire catalog:
lupus001: lupus001_FLAIR_reg+bias+brain.nii.gz lupus001_FLAIR_reg+bias.nii.gz lupus001_T1_reg+bias+brain.nii.gz lupus001_T1_reg+bias.nii.gz lupus001_T2_reg+bias+brain.nii.gz lupus001_T2_reg+bias.nii.gz lupus001_brain_mask.nii.gz lupus001_lesion_manual_reg.nii.gz

lupus002: lupus002_FLAIR_reg+bias+brain.nii.gz lupus002_FLAIR_reg+bias.nii.gz lupus002_T1_reg+bias+brain.nii.gz lupus002_T1_reg+bias.nii.gz lupus002_T2_reg+bias+brain.nii.gz lupus002_T2_reg+bias.nii.gz lupus002_brain_mask.nii.gz lupus002_lesion_manual_reg.nii.gz lupus003: lupus003_FLAIR_reg+bias+brain.nii.gz lupus003_FLAIR_reg+bias.nii.gz

lupus003_T1_reg+bias+brain.nii.gz lupus003_T1_reg+bias.nii.gz lupus003_T2_reg+bias+brain.nii.gz lupus003_T2_reg+bias.nii.gz lupus003_brain_mask.nii.gz lupus003_lesion_manual_reg.nii.gz lupus004: lupus004_FLAIR_reg+bias+brain.nii.gz

lupus004_FLAIR_reg+bias.nii.gz lupus004_T1_reg+bias+brain.nii.gz lupus004_T1_reg+bias.nii.gz lupus004_T2_reg+bias+brain.nii.gz lupus004_T2_reg+bias.nii.gz lupus004_brain_mask.nii.gz lupus004_lesion_manual_reg.nii.gz lupus005:

lupus005_FLAIR_reg+bias+brain.nii.gz lupus005_FLAIR_reg+bias.nii.gz lupus005_T1_reg+bias+brain.nii.gz lupus005_T1_reg+bias.nii.gz lupus005_T2_reg+bias+brain.nii.gz lupus005_T2_reg+bias.nii.gz lupus005_brain_mask.nii.gz lupus005_lesion_manual_reg.nii.gz

=== Data Contact ===

H Jeremy Bockholt<br />
Director, Neuroinformatics<br />
The Mind Research Network<br />
jbockholt at mrn.org

Mark Scully<br />
Software Engineer<br />
Psychiatry Deptartment<br />
University of Iowa<br />
mark-scully at uiowa.edu

DBP2:MIND:Roadmap

2011-01-18T17:09:45Z

Mscully: /* Team and Institute */

Back to [[NA-MIC_Internal_Collaborations|NA-MIC Internal Collaborations]], [[DBP2:MIND|MIND DBP 2]]
__NOTOC__
=Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus=

[[Image:BrainVentriclesAndLesions.png‎|thumb|280px|Lesion volumes in yellow with ventricles and brain slice]]
=='''Objective'''==
This page describes the technology roadmap for lesion analysis in the NA-MIC Kit. Our objective is to create an end-to-end application allowing individual analysis of white matter lesions. This workflow applied to lupus patients is one of goals of the [[DBP2:MIND:Introduction|MIND DBP]]. The basic components necessary for this project are:
* '''Registration''': co-registration of T1-weighted, T2-weighted, and FLAIR images
* '''Tissue segmentation''': Should be multi-modality, correcting for intensity inhomogeneity and work on non-skull-stripped data.
* '''Lesion Localization''': Each unique lesion should be detected and anatomical location summarized
* '''Lesion Load Measurement''': Measure volume of each lesion, summarize lesion load by regions
* '''Time Series Analysis of white matter lesions''': Compare lesions between multiple scans taken over time.
* '''Multi-scale Analysis of white matter lesions''': Combine DTI, anatomical, and functional scans when analyzing lupus subjects.
* '''Tutorial''': Documentation will be written for a tutorial and sample data sets will be provided

=='''Roadmap'''==
We obtained gray matter, white matter, CSF, and lesion maps for each subject based on T1-weighted, T2-weighted, and FLAIR images. Ultimately, the NA-MIC Kit will provide a workflow for individual and group analysis of lesions. It will be implemented as a set of Slicer3 modules that can be used interactively within the Slicer3 application as well as in batch on a computing cluster using [http://batchmake.org/ BatchMake].

<center>
{|
|[[Image:Scully Figure3.jpg|thumb|400px|A. FLAIR with predicted probability of being lesion, B. FLAIR with manual segmentation, C. FLAIR with predicted probability after thresholding]]
|[[Image:TractsLesionZoomOverlay.png‎|thumb|380px|White Matter Lesion Disruption of a U fiber]]
|}
{|
|[[Image:ComapareViewL1L2Overview.jpg|thumb|400px| Compare Layout overview with baseline FLAIR image on top and followup FLAIR on bottom. Each image is overlaid with that time point's predicted lesion segmentation.]]
|[[Image:CompareViewLDiffZoomedIn.jpg|thumb|400px| Compare Layout zoomed in. Baseline FLAIR on top and followup on bottom. Images overlaid with a label map that represents changes in lesion. Yellow represents lesion that's unchanged between baseline and followup, red represents new lesion in the followup, and blue represents lesion present at baseline that is no longer present at followup. ]]
| [[Image:MIND-DBPLesionClassZoomDetail.png|thumb|158px| Zoomed detail. ]]
|}
</center>

===Software===
*We have a very active project for this pipeline on the NITRC resource [http://www.nitrc.org/frs/?group_id=180 3DSlicerLupusLesionModule]
*The module can be checked out in Slicer3.6 using the extension manager or downloaded [http://www.nitrc.org/frs/download.php/570/LesionSegmentationApplications.tgz here].
*Source code is available via [http://www.nitrc.org/plugins/scmcvs/cvsweb.php/lupuslesion/LesionSegmentationApplications/?cvsroot=lupuslesion cvs].

=== Tutorial ===
* A step-by-step guide for one example lupus case is available [http://www.nitrc.org/frs/download.php/571/Slicer3Training_WhiteMatterLesions_v2.0.ppt.pdf here].
* The data needed to run the tutorial is available [http://www.nitrc.org/frs/download.php/569/LesionSegmentationTutorialData.tgz here].

=== Schedule ===
* 06/21/2010 - 06/25/2010 Release new version of module and tutorial including directions and data for longitudinal analysis at the Summer project week
* 04/20/2010 Began updating module to use ITK review statistics
* 03/19/2010 Segmentation Method paper published in Frontiers in Human Neuroscience
* 01/04/2010 - 01/08/2010 Demonstrated longitudinal analysis and some of the multiscale work at the Winter Project Week / All Hands Meeting
* 12/15/2009 Developed longitudinal analysis method
* 11/18/2009 Submitted paper on novel lesion segmentation method to Frontiers in Human Neuroscience
* 08/15/2009 Expanded lesion model to include additional cases
* 06/22/2009 - 06/26/2009 Summer Project Week
* 06/18/2009 - 06/23/2009 Attended Human Brain Mapping Conference with submitted abstract on lesion classification using novel method
* 03/25/2009 - 04/02/2009 AAN conference outreach activity
* 03/01/2009 Released final version of the novel lesion segmentation method as a Slicer module
* 01/11/2009 Submitted abstract on novel lesion method for HBM 2009
* 01/06/2009 Initial version of the novel lesion segmentation method released as slicer module.
* 01/05/2009 - 01/09/2009 Winter Project Week / All Hands Meeting
* 11/15/2008 - 11/19/2008 Abstract on initial version of the novel lesion method submitted to Society For Neuroscience conference and held a Conference / Outreach activity on the Slicer lesion segmentation tool.
* 09/11/2008 Began development on novel lesion segmentation method
* 09/06/2008 - 09/10/2008 Participated in the MS lesion segmentation challenge, part of the 3D Segmentation in the Clinic: A Grand Challenge II
* 08/14/2008 EMSegment has been run against collected lupus cases. Segmentations have improved but are still unusable
* 07/01/2008 Made tutorial and sample data available to the scientific community
* 06/23/2008 - 06/27/2008 Presented lesion segmentation tutorial at the Summer Project Week
* 05/12/2008 Submitted SFN abstract on a lesion segmentation method based on Vince Magnotta's work
* 04/01/2008 Gasparovic has manually traced all tutorial cases with lesions using T2/Flair images following tracing guidelines and a qualitative neuroradiological review report
* 03/31/2008 Completed collection of 5 lupus subjects on clinical sequence and optimized 3T sequence
* 03/17/2008 Applied itkEMS to sample lesion cases, results are shown [[DBP2:MIND:itkEMSResults|here]]
* 03/15/2008 Applied Vince Magnotta's lesions segmentation method to sample lesion cases, results are shown [[DBP2:MIND:itkBayesianLesion|here]]
* 02/05/2008 Created intensity standardization method
* 01/10/2008 Performed initial segmentations using EMSegment and submitted bug reports
* 01/07/2008 - 01/11/2008 Winter Project Week / All Hands Meeting
* 10/15/2007 optimized sequences for T1, T2, and FLAIR for Siemens 3T Trio Tim scanner
* 08/01/2007 Created project requirements and architecture
* 06/25/2007 - 06/29/2007 Attended Project Week

=== '''Publications''' ===
* H. J. Bockholt, V. A. Magnotta, M. Scully, C. Gasparovic, B. Davis, K. Pohl, R. Whitaker, S. Pieper, C. Roldan, R. Jung, R. Hayek, W. Sibbitt, J. Sharrar, P. Pellegrino, R. Kikinis. A novel automated method for classification of white matter lesions in systemic lupus erythematosus. Presented at the 38th annual meeting of the Society for Neuroscience, Washingto, DC, 15 – 19 November 2008
* Scully M., Magnotta V., Gasparovic C., Pelligrimo P., Feis D., Bockholt H.J. 3D Segmentation In The Clinic: A Grand Challenge II at MICCAI 2008 - MS Lesion Segmentation. IJ - 2008 MICCAI Workshop - MS Lesion Segmentation. Available http://grand-challenge2008.bigr.nl/proceedings/pdfs/msls08/282_Scully.pdf
* H Jeremy Bockholt, Josef Ling, Mark Scully, Adam Scott, Susan Lane, Vincent Magnotta, Tonya White, Kelvin Lim, Randy Gollub, Vince Calhoun. Real-time Web-scale Image Annotation for Semantic-based Retrieval of Neuropsychiatric Research Images. Presented at the 14th Annual Meeting of the Organization for Human Brain Mapping, Melbourne, Australia, 15 – 19 June, 2008.
* H Jeremy Bockholt, Sumner Williams, Mark Scully, Vincent Magnotta, Randy Gollub, John Lauriello, Kelvin Lim, Tonya White, Rex Jung, Charles Schulz, Nancy Andreasen, Vince Calhoun. The MIND Clinical Imaging Consortium as an application for novel comprehensive quality assurance procedures in a multi-site heterogeneous clinical research study. Presented at the 14th Annual Meeting of the Organization for Human Brain Mapping, Melbourne, Australia, 15 – 19 June, 2008.
* M Scully, B H Anderson, C Gasparovic, V A Magnotta, S Pieper, R Kikinis, P Pellegrino, T Lane, H J Bockholt. A Synergistic Combination of Supervised Machine Learning Methods for Analysis of White Matter Lesions in Neuropsychiatric Systemic Lupus Erythematosus. Presented at the 15th Annual Meeting of the Organization for Human Brain Mapping, San Francisco June, 2009.
* Bockholt HJ, Scully M, Courtney W, Rachakonda S, Scott A, Caprihan A, Fries J, Kalyanam R, Segall J, de la Garza R, Lane S and Calhoun VD (2009) Mining the mind research network: a novel framework for exploring large scale, heterogeneous translational neuroscience research data sources. Front. Neuroinform. 3:36. doi:10.3389/neuro.11.036.2009
* Scully M, Anderson B, Lane T, Gasparovic C, Magnotta V, Sibbitt W, Roldan C, Kikinis R and Bockholt HJ (2010) An automated method for segmenting white matter lesions through multi-level morphometric feature classification with application to lupus. Front. Hum. Neurosci. 4:27. doi:10.3389/fnhum.2010.00027. Available [http://www.frontiersin.org/humanneuroscience/paper/10.3389/fnhum.2010.00027/ here]
* Scully, M., Lane, T., Gasparovic, C., Magnotta, V., Sibbitt, W., Roldan,C. , Kikinis, R., Bockholt, H. J. An Automated Method For Longitudinal Analysis of White Matter Lesions in Lupus (''in preparation'' for submission).
* Bockholt, H.J., Gasparovic, C., Scully, M., Magnotta, V., Sibbitt, W., Kikinis, R., Roldan,C. A novel white matter lesion analysis for improved clinical application in lupus. (''in preparation'' for submission).

=== '''Team and Institute''' ===
* Co-PI: [http://www.mrn.org/principal-investigators/h-jeremy-bockholt H Jeremy Bockholt] (jbockholt at mrn.org)
* Co-PI: [http://www.mrn.org/principal-investigators/charles-gasparovic-ph-d Charles Gasparovic] (chuck at unm.edu)
* Software Engineer: Mark Scully (mark-scully at uiowa.edu)
* NA-MIC Engineering Contact: [http://www.na-mic.org/Wiki/index.php/User:Pieper Steve Pieper], Isomics
* NA-MIC Algorithms Contact: Ross Whitaker, Utah
* Host Institues: The [http://www.mrn.org Mind Research Network] and [http://www.unm.edu The University of New Mexico]

[[Category:Slicer]] [[Category:Segmentation]] [[Category:Registration]]