NAMIC Wiki - User contributions [en]

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-05-20T20:36:20Z

Mathieuc: /* Pipeline overview */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-04-27T19:04:30Z

Mathieuc: /* In progress */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-04-06T17:28:44Z

Mathieuc:

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-26T20:07:25Z

Mathieuc: /* Download and install the NeuroLib */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|400px|ARCTIC Logo|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developed: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== ARCTIC Download ==
=== Source code available with CVS ===

====Required softwares====

* Install required softwares to compile the NeuroLib
- [http://www.cmake.org/cmake/resources/software.html| CMake]

- [http://www.batchmake.org/batchmake/resources/software.html| BatchMake] (v 1.0.8 needed, use cvs access)

- [http://www.fltk.org/software.php| FLTK]

- [http://www.slicer.org/DownloadSlicer.php/Nightly| Slicer Nighly Build]

====Download and install the NeuroLib====

* Create and go to a NeuroLib/ directory
mkdir NeuroLib
cd NeuroLib
* Make the following commands :
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot login (press Enter for password)
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot co -P NeuroLib
* Create and go to a Neurolib-build/ directory
mkdir NeuroLib-build
cd NeuroLib-build
* Start the compilation while launching 'ccmake'
ccmake ../NeuroLib
*Configure the compilation
Set ARCTIC at "ON"
Press 'c' to start the configuration

=== Executables and tutorial dataset ===
Available on NITRC : http://www.nitrc.org/projects/arctic/

== Complementary Downloads ==

=== Pediatric atlas ===
Available on MIDAS : http://www.insight-journal.org/midas/item/view/2277

=== Tutorials ===
• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3-Plugins-Directory:Slicer3-Bin-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3-Plugins-Directory:Slicer3-Bin-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Bin-Directory" and "Slicer3-Bin-Directory" in the PATH.

Add libraries to the LD_LIBRARY_PATH variable
-tcsh usage : setenv SLICERLIBPATH Slicer-nightly-build/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${SLICERLIBPATH}/BatchMake:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/GenerateCLP:${SLICERLIBPATH}/GenerateLM:${SLICERLIBPATH}/IGT:${SLICERLIBPATH}/igtl:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ITKCommandIO:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/LoadableModule:${SLICERLIBPATH}/MGHImageIO:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/MRMLIDImageIO:${SLICERLIBPATH}/OpenIGTLink:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/Qdec:${SLICERLIBPATH}/RemoteIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/tclap:${SLICERLIBPATH}/TclTk/lib:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/vtkTeem
-bash usage : export SLICERLIBPATH=Slicer-nightly-build/lib
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${SLICERLIBPATH}/BatchMake:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/GenerateCLP:${SLICERLIBPATH}/GenerateLM:${SLICERLIBPATH}/IGT:${SLICERLIBPATH}/igtl:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ITKCommandIO:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/LoadableModule:${SLICERLIBPATH}/MGHImageIO:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/MRMLIDImageIO:${SLICERLIBPATH}/OpenIGTLink:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/Qdec:${SLICERLIBPATH}/RemoteIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/tclap:${SLICERLIBPATH}/TclTk/lib:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/vtkTeem

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

ARCTIC can be use with two different input modes.

==== Raw Image Mode ====

Inputs: T1-weighted image, T1-weighted atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/ --atlas Atlas.gipl --atlasParcellation Parcellation.gipl

Complementary flags
--T2 Image_T2.gipl / --pd Image_PD.gipl : T2 and/or Pd-weighted image(s) can be added to improve tissue segmentation
--orientation RAI : if the orientation of your file(s) is different than the default value (RAI), add this flag to set the right orientation
--atlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
--atlasType T1 : if the type of your tissue segmentation atlas is different than T1 (default value)
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

==== Segmented Image Mode ====

Inputs: label image, regional atlas (parcellation map)

ARCTIC --label label_image.gipl --rawImage raw_image.gipl --atlas Atlas.gipl --atlasParcellation Parcellation.gipl
Notice : the "raw_image.gipl" file is a MRI image of the case. It can be a T1-weighted image as well as a T2 or a PD.

Complementary flags
--WMLabel 1 / --GMLabel 2 / --CSFLabel 3 : if tour label are different than the default value
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation
:* ARCTIC source code (SVN, CVS) available to the community

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* Mac and windows executables available on to the community through NITRC

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-26T18:48:17Z

Mathieuc: /* ARCTIC (Automatic Regional Cortical ThICkness) usage: */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|400px|ARCTIC Logo|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developed: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== ARCTIC Download ==
=== Source code available with CVS ===

====Required softwares====

* Install required softwares to compile the NeuroLib
- [http://www.cmake.org/cmake/resources/software.html| CMake]

- [http://www.batchmake.org/batchmake/resources/software.html| BatchMake] (v 1.0.8 needed, use cvs access)

- [http://www.fltk.org/software.php| FLTK]

- [http://www.slicer.org/DownloadSlicer.php/Nightly| Slicer Nighly Build]

====Download and install the NeuroLib====

* Create and go to a NeuroLib/ directory
mkdir NeuroLib
cd NeuroLib
* Make the following commands :
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot login (press Enter for password)
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot co NeuroLib
* Create and go to a Neurolib-build/ directory
mkdir NeuroLib-build
cd NeuroLib-build
* Start the compilation while launching 'ccmake'
ccmake ../NeuroLib
*Configure the compilation
Set ARCTIC at "ON"
Press 'c' to start the configuration

=== Executables and tutorial dataset ===
Available on NITRC : http://www.nitrc.org/projects/arctic/

== Complementary Downloads ==

=== Pediatric atlas ===
Available on MIDAS : http://www.insight-journal.org/midas/item/view/2277

=== Tutorials ===
• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3-Plugins-Directory:Slicer3-Bin-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3-Plugins-Directory:Slicer3-Bin-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Bin-Directory" and "Slicer3-Bin-Directory" in the PATH.

Add libraries to the LD_LIBRARY_PATH variable
-tcsh usage : setenv SLICERLIBPATH Slicer-nightly-build/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${SLICERLIBPATH}/BatchMake:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/GenerateCLP:${SLICERLIBPATH}/GenerateLM:${SLICERLIBPATH}/IGT:${SLICERLIBPATH}/igtl:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ITKCommandIO:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/LoadableModule:${SLICERLIBPATH}/MGHImageIO:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/MRMLIDImageIO:${SLICERLIBPATH}/OpenIGTLink:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/Qdec:${SLICERLIBPATH}/RemoteIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/tclap:${SLICERLIBPATH}/TclTk/lib:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/vtkTeem
-bash usage : export SLICERLIBPATH=Slicer-nightly-build/lib
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${SLICERLIBPATH}/BatchMake:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/GenerateCLP:${SLICERLIBPATH}/GenerateLM:${SLICERLIBPATH}/IGT:${SLICERLIBPATH}/igtl:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ITKCommandIO:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/LoadableModule:${SLICERLIBPATH}/MGHImageIO:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/MRMLIDImageIO:${SLICERLIBPATH}/OpenIGTLink:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/Qdec:${SLICERLIBPATH}/RemoteIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/tclap:${SLICERLIBPATH}/TclTk/lib:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/vtkTeem

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

ARCTIC can be use with two different input modes.

==== Raw Image Mode ====

Inputs: T1-weighted image, T1-weighted atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/ --atlas Atlas.gipl --atlasParcellation Parcellation.gipl

Complementary flags
--T2 Image_T2.gipl / --pd Image_PD.gipl : T2 and/or Pd-weighted image(s) can be added to improve tissue segmentation
--orientation RAI : if the orientation of your file(s) is different than the default value (RAI), add this flag to set the right orientation
--atlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
--atlasType T1 : if the type of your tissue segmentation atlas is different than T1 (default value)
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

==== Segmented Image Mode ====

Inputs: label image, regional atlas (parcellation map)

ARCTIC --label label_image.gipl --rawImage raw_image.gipl --atlas Atlas.gipl --atlasParcellation Parcellation.gipl
Notice : the "raw_image.gipl" file is a MRI image of the case. It can be a T1-weighted image as well as a T2 or a PD.

Complementary flags
--WMLabel 1 / --GMLabel 2 / --CSFLabel 3 : if tour label are different than the default value
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation
:* ARCTIC source code (SVN, CVS) available to the community

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* Mac and windows executables available on to the community through NITRC

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-24T15:35:23Z

Mathieuc: /* Prerequities */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|400px|ARCTIC Logo|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developed: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== ARCTIC Download ==
=== Source code available with CVS ===

====Required softwares====

* Install required softwares to compile the NeuroLib
- [http://www.cmake.org/cmake/resources/software.html| CMake]

- [http://www.batchmake.org/batchmake/resources/software.html| BatchMake] (v 1.0.8 needed, use cvs access)

- [http://www.fltk.org/software.php| FLTK]

- [http://www.slicer.org/DownloadSlicer.php/Nightly| Slicer Nighly Build]

====Download and install the NeuroLib====

* Create and go to a NeuroLib/ directory
mkdir NeuroLib
cd NeuroLib
* Make the following commands :
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot login (press Enter for password)
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot co NeuroLib
* Create and go to a Neurolib-build/ directory
mkdir NeuroLib-build
cd NeuroLib-build
* Start the compilation while launching 'ccmake'
ccmake ../NeuroLib
*Configure the compilation
Set ARCTIC at "ON"
Press 'c' to start the configuration

=== Executables and tutorial dataset ===
Available on NITRC : http://www.nitrc.org/projects/arctic/

== Complementary Downloads ==

=== Pediatric atlas ===
Available on MIDAS : http://www.insight-journal.org/midas/item/view/2277

=== Tutorials ===
• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Add libraries to the LD_LIBRARY_PATH variable
-tcsh usage : setenv SLICERLIBPATH Slicer-nightly-build/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${SLICERLIBPATH}/BatchMake:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/GenerateCLP:${SLICERLIBPATH}/GenerateLM:${SLICERLIBPATH}/IGT:${SLICERLIBPATH}/igtl:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ITKCommandIO:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/LoadableModule:${SLICERLIBPATH}/MGHImageIO:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/MRMLIDImageIO:${SLICERLIBPATH}/OpenIGTLink:${SLICERLIBPATH}/Python:${SLICERLIBPATH}/Qdec:${SLICERLIBPATH}/RemoteIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/tclap:${SLICERLIBPATH}/TclTk:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/vtkTeem
-bash usage : export SLICERLIBPATH=Slicer-nightly-build/lib
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${SLICERLIBPATH}/BatchMake:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/GenerateCLP:${SLICERLIBPATH}/GenerateLM:${SLICERLIBPATH}/IGT:${SLICERLIBPATH}/igtl:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ITKCommandIO:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/LoadableModule:${SLICERLIBPATH}/MGHImageIO:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/MRMLIDImageIO:${SLICERLIBPATH}/OpenIGTLink:${SLICERLIBPATH}/Python:${SLICERLIBPATH}/Qdec:${SLICERLIBPATH}/RemoteIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/tclap:${SLICERLIBPATH}/TclTk:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/vtkTeem

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

ARCTIC can be use with two different input modes.

==== Raw Image Mode ====

Inputs: T1-weighted image, T1-weighted atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/ --atlas Atlas.gipl --atlasParcellation Parcellation.gipl

Complementary flags
--T2 Image_T2.gipl / --pd Image_PD.gipl : T2 and/or Pd-weighted image(s) can be added to improve tissue segmentation
--orientation RAI : if the orientation of your file(s) is different than the default value (RAI), add this flag to set the right orientation
--atlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
--atlasType T1 : if the type of your tissue segmentation atlas is different than T1 (default value)
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

==== Segmented Image Mode ====

Inputs: label image, regional atlas (parcellation map)

ARCTIC --label label_image.gipl --rawImage raw_image.gipl --atlas Atlas.gipl --atlasParcellation Parcellation.gipl
Notice : the "raw_image.gipl" file is a MRI image of the case. It can be a T1-weighted image as well as a T2 or a PD.

Complementary flags
--WMLabel 1 / --GMLabel 2 / --CSFLabel 3 : if tour label are different than the default value
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation
:* ARCTIC source code (SVN, CVS) available to the community

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* Mac and windows executables available on to the community through NITRC

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-23T20:43:59Z

Mathieuc: /* ARCTIC (Automatic Regional Cortical ThICkness) usage: */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|400px|ARCTIC Logo|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developed: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== ARCTIC Download ==
=== Source code available with CVS ===

====Required softwares====

* Install required softwares to compile the NeuroLib
- [http://www.cmake.org/cmake/resources/software.html| CMake]

- [http://www.batchmake.org/batchmake/resources/software.html| BatchMake] (v 1.0.8 needed, use cvs access)

- [http://www.fltk.org/software.php| FLTK]

- [http://www.slicer.org/DownloadSlicer.php/Nightly| Slicer Nighly Build]

====Download and install the NeuroLib====

* Create and go to a NeuroLib/ directory
mkdir NeuroLib
cd NeuroLib
* Make the following commands :
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot login (press Enter for password)
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot co NeuroLib
* Create and go to a Neurolib-build/ directory
mkdir NeuroLib-build
cd NeuroLib-build
* Start the compilation while launching 'ccmake'
ccmake ../NeuroLib
*Configure the compilation
Set ARCTIC at "ON"
Press 'c' to start the configuration

=== Executables and tutorial dataset ===
Available on NITRC : http://www.nitrc.org/projects/arctic/

== Complementary Downloads ==

=== Pediatric atlas ===
Available on MIDAS : http://www.insight-journal.org/midas/item/view/2277

=== Tutorials ===
• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Add libraries to the LD_LIBRARY_PATH variable
-tcsh usage : setenv SLICERLIBPATH Slicer-nightly-build/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${SLICERLIBPATH}/TEEM-1.9:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/vtkTeem:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/BatchMake
-bash usage : export SLICERLIBPATH=Slicer-nightly-build/lib
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${SLICERLIBPATH}/TEEM-1.9:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/vtkTeem:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/BatchMake

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

ARCTIC can be use with two different input modes.

==== Raw Image Mode ====

Inputs: T1-weighted image, T1-weighted atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/ --atlas Atlas.gipl --atlasParcellation Parcellation.gipl

Complementary flags
--T2 Image_T2.gipl / --pd Image_PD.gipl : T2 and/or Pd-weighted image(s) can be added to improve tissue segmentation
--orientation RAI : if the orientation of your file(s) is different than the default value (RAI), add this flag to set the right orientation
--atlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
--atlasType T1 : if the type of your tissue segmentation atlas is different than T1 (default value)
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

==== Segmented Image Mode ====

Inputs: label image, regional atlas (parcellation map)

ARCTIC --label label_image.gipl --rawImage raw_image.gipl --atlas Atlas.gipl --atlasParcellation Parcellation.gipl
Notice : the "raw_image.gipl" file is a MRI image of the case. It can be a T1-weighted image as well as a T2 or a PD.

Complementary flags
--WMLabel 1 / --GMLabel 2 / --CSFLabel 3 : if tour label are different than the default value
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation
:* ARCTIC source code (SVN, CVS) available to the community

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* Mac and windows executables available on to the community through NITRC

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-23T20:33:56Z

Mathieuc: /* Source code available with CVS */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|400px|ARCTIC Logo|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developed: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== ARCTIC Download ==
=== Source code available with CVS ===

====Required softwares====

* Install required softwares to compile the NeuroLib
- [http://www.cmake.org/cmake/resources/software.html| CMake]

- [http://www.batchmake.org/batchmake/resources/software.html| BatchMake] (v 1.0.8 needed, use cvs access)

- [http://www.fltk.org/software.php| FLTK]

- [http://www.slicer.org/DownloadSlicer.php/Nightly| Slicer Nighly Build]

====Download and install the NeuroLib====

* Create and go to a NeuroLib/ directory
mkdir NeuroLib
cd NeuroLib
* Make the following commands :
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot login (press Enter for password)
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot co NeuroLib
* Create and go to a Neurolib-build/ directory
mkdir NeuroLib-build
cd NeuroLib-build
* Start the compilation while launching 'ccmake'
ccmake ../NeuroLib
*Configure the compilation
Set ARCTIC at "ON"
Press 'c' to start the configuration

=== Executables and tutorial dataset ===
Available on NITRC : http://www.nitrc.org/projects/arctic/

== Complementary Downloads ==

=== Pediatric atlas ===
Available on MIDAS : http://www.insight-journal.org/midas/item/view/2277

=== Tutorials ===
• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Add libraries to the LD_LIBRARY_PATH variable
-tcsh usage : setenv SLICERLIBPATH Slicer-nightly-build/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${SLICERLIBPATH}/TEEM-1.9:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/vtkTeem:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/BatchMake
-bash usage : export SLICERLIBPATH=Slicer-nightly-build/lib
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${SLICERLIBPATH}/TEEM-1.9:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/vtkTeem:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/BatchMake

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

ARCTIC can be use with two different input modes.

==== Raw Image Mode ====

Inputs: T1-weighted image, T1-weighted atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/ --atlas Atlas.gipl --atlasParcellation Parcellation.gipl

Complementary flags
--T2 Image_T2.gipl / --pd Image_PD.gipl : T2 and/or Pd-weighted image(s) can be added to improve tissue segmentation
--orientation RAI : if the orientation of your file(s) is different than the default value (RAI), add this flag to set the right orientation
--atlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
--atlasType T1 : if the type of your tissue segmentation atlas is different than T1 (default value)
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

==== Segmented Image Mode ====

Inputs: label image, regional atlas (parcellation map)

ARCTIC --label label_image.gipl --rawImage raw_image.gipl --atlas Atlas.gipl --atlasParcellation Parcellation.gipl
Notice : the "raw_image.gipl" file is a MRI image of the case. It can be a T1-weighted image as well as a T2 or a PD.

Complementary flags
--WMLabel 1 / --GMLabel 2 / --CSFLabel 3 :

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation
:* ARCTIC source code (SVN, CVS) available to the community

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* Mac and windows executables available on to the community through NITRC

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-23T17:01:05Z

Mathieuc: /* Prerequities */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|400px|ARCTIC Logo|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developed: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== ARCTIC Download ==
=== Source code available with CVS ===
* Create and go to a NeuroLib/ directory
mkdir NeuroLib
cd NeuroLib
* Make the following commands :
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot login (press Enter for password)
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot co NeuroLib
* Be sure that the 2.6 version of CMake is installed on your computer. [http://www.cmake.org/cmake/resources/software.html| ‏If not download it here]
* Create and go to a Neurolib-build/ directory
mkdir NeuroLib-build
cd NeuroLib-build
* Start the compilation while launching 'ccmake'
ccmake ../NeuroLib
*Configure the compilation
Set ARCTIC at "ON"
Press 'c' to start the configuration

=== Executables and tutorial dataset ===
Available on NITRC : http://www.nitrc.org/projects/arctic/

== Complementary Downloads ==

=== Pediatric atlas ===
Available on MIDAS : http://www.insight-journal.org/midas/item/view/2277

=== Tutorials ===
• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Add libraries to the LD_LIBRARY_PATH variable
-tcsh usage : setenv SLICERLIBPATH Slicer-nightly-build/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${SLICERLIBPATH}/TEEM-1.9:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/vtkTeem:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/BatchMake
-bash usage : export SLICERLIBPATH=Slicer-nightly-build/lib
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${SLICERLIBPATH}/TEEM-1.9:${SLICERLIBPATH}/vtk-5.2:${SLICERLIBPATH}:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/vtkTeem:${SLICERLIBPATH}/Teem-1.10.0:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/BatchMake

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

ARCTIC can be use with two different input modes.

==== Raw Image Mode ====

Inputs: T1-weighted image, T1-weighted atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/ --atlas Atlas.gipl --atlasParcellation Parcellation.gipl

Complementary flags
--T2 Image_T2.gipl / --pd Image_PD.gipl : T2 and/or Pd-weighted image(s) can be added to improve tissue segmentation
--orientation RAI : if the orientation of your file(s) is different than the default value (RAI), add this flag to set the right orientation
--atlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
--atlasType T1 : if the type of your tissue segmentation atlas is different than T1 (default value)
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

==== Segmented Image Mode ====

Inputs: label image, regional atlas (parcellation map)

ARCTIC --label label_image.gipl --rawImage raw_image.gipl --atlas Atlas.gipl --atlasParcellation Parcellation.gipl
Notice : the "raw_image.gipl" file is a MRI image of the case. It can be a T1-weighted image as well as a T2 or a PD.

Complementary flags
--WMLabel 1 / --GMLabel 2 / --CSFLabel 3 :

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation
:* ARCTIC source code (SVN, CVS) available to the community

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* Mac and windows executables available on to the community through NITRC

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T21:08:48Z

Mathieuc: /* Command line execution */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|400px|ARCTIC Logo|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developed: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== ARCTIC Download ==
=== Source code available with CVS ===
* Create and go to a NeuroLib/ directory
mkdir NeuroLib
cd NeuroLib
* Make the following commands :
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot login (press Enter for password)
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot co NeuroLib
* Be sure that the 2.6 version of CMake is installed on your computer. [http://www.cmake.org/cmake/resources/software.html| ‏If not download it here]
* Create and go to a Neurolib-build/ directory
mkdir NeuroLib-build
cd NeuroLib-build
* Start the compilation while launching 'ccmake'
ccmake ../NeuroLib
*Configure the compilation
Set ARCTIC at "ON"
Press 'c' to start the configuration

=== Executables and tutorial dataset ===
Available on NITRC : http://www.nitrc.org/projects/arctic/

== Complementary Downloads ==

=== Pediatric atlas ===
Available on MIDAS : http://www.insight-journal.org/midas/item/view/2277

=== Tutorials ===
• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Add libraries to the LD_LIBRARY_PATH variable
-tcsh usage : setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:Slicer-nightly-build/lib/InsightToolkit
-bash usage : export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:Slicer-nightly-build/lib/InsightToolkit

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

ARCTIC can be use with two different input modes.

==== Raw Image Mode ====

Inputs: T1-weighted image, T1-weighted atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/ --atlas Atlas.gipl --atlasParcellation Parcellation.gipl

Complementary flags
--T2 Image_T2.gipl / --pd Image_PD.gipl : T2 and/or Pd-weighted image(s) can be added to improve tissue segmentation
--orientation RAI : if the orientation of your file(s) is different than the default value (RAI), add this flag to set the right orientation
--atlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
--atlasType T1 : if the type of your tissue segmentation atlas is different than T1 (default value)
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder
--SaveWM WMCorticalThicknessMap.gipl / --SaveGM GMCorticalThicknessMap.gipl : those flags are used to save a volume with information of the average cortical thickness on WM/GM boundary(ies), the fileName needed is a path with the name of the output volume

==== Segmented Image Mode ====

Inputs: label image, regional atlas (parcellation map)

ARCTIC --label label_image.gipl --rawImage raw_image.gipl --atlas Atlas.gipl --atlasParcellation Parcellation.gipl
Notice : the "raw_image.gipl" file is a MRI image of the case. It can be a T1-weighted image as well as a T2 or a PD.

Complementary flags
--WMLabel 1 / --GMLabel 2 / --CSFLabel 3 :

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation
:* ARCTIC source code (SVN, CVS) available to the community

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* Mac and windows executables available on to the community through NITRC

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T20:42:01Z

Mathieuc: /* Command line execution */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|400px|ARCTIC Logo|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developed: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== ARCTIC Download ==
=== Source code available with CVS ===
* Create and go to a NeuroLib/ directory
mkdir NeuroLib
cd NeuroLib
* Make the following commands :
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot login (press Enter for password)
cvs -d :pserver:anonymous@demeter.ia.unc.edu:/cvsroot co NeuroLib
* Be sure that the 2.6 version of CMake is installed on your computer. [http://www.cmake.org/cmake/resources/software.html| ‏If not download it here]
* Create and go to a Neurolib-build/ directory
mkdir NeuroLib-build
cd NeuroLib-build
* Start the compilation while launching 'ccmake'
ccmake ../NeuroLib
*Configure the compilation
Set ARCTIC at "ON"
Press 'c' to start the configuration

=== Executables and tutorial dataset ===
Available on NITRC : http://www.nitrc.org/projects/arctic/

== Complementary Downloads ==

=== Pediatric atlas ===
Available on MIDAS : http://www.insight-journal.org/midas/item/view/2277

=== Tutorials ===
• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Add libraries to the LD_LIBRARY_PATH variable
-tcsh usage : setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:Slicer-nightly-build/lib/InsightToolkit
-bash usage : export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:Slicer-nightly-build/lib/InsightToolkit

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

Inputs: T1-weighted image, T1-weighted atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/ --atlas Atlas.gipl --atlasParcellation Parcellation.gipl (--SaveWM WMCorticalThicknessMap.gipl --SaveGM GMCorticalThicknessMap.gipl)
Notices : - for both flags "SaveWM" and "SaveGM", the fileName needed is a path with the name of the output volume.

Complementary flags
--T2 Image_T2.gipl / --pd Image_PD.gipl : T2 and/or Pd-weighted image(s) can be added to improve tissue segmentation
--orientation RAI : if the orientation of your file(s) is different than the default value (RAI), add this flag to set the right orientation
--atlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
--outputDir output_directory/ : if you want to select the output directory, add this flag and indicate the path an existing folder

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation
:* ARCTIC source code (SVN, CVS) available to the community

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* Mac and windows executables available on to the community through NITRC

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T17:56:26Z

Mathieuc: /* Planning */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T17:53:55Z

Mathieuc: /* Download */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T17:52:07Z

Mathieuc: /* Prerequities */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T17:51:47Z

Mathieuc: /* Prerequities */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T17:48:42Z

Mathieuc: /* Command line execution */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T17:47:50Z

Mathieuc: /* Command line execution */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-20T17:47:27Z

Mathieuc: /* ARCTIC (Automatic Regional Cortical ThICkness) usage: */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T21:33:23Z

Mathieuc: /* Source code available with CVS */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T21:15:52Z

Mathieuc: /* Source code available with CVS */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T21:08:39Z

Mathieuc: /* Source code available with CVS */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T21:08:10Z

Mathieuc:

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T21:03:32Z

Mathieuc: /* Source code available with CVS */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T20:44:41Z

Mathieuc: /* Download */

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T20:14:54Z

Mathieuc:

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T19:57:01Z

Mathieuc:

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-19T19:56:07Z

Mathieuc:

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]

[[Image:ArcticLogo.png|thumb|250px|Screenshot of the application|right]]

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developped: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 external module)
:* '''4. Statistics'''
:** Generate spreesheats with volume informations
:** Tools: ImageMath, ImageStat (UNC Slicer3 external modules)
:* '''5. Mesh Creation'''
:** Generation of white matter and grey matter meshes
:** Tool: ModelMaker (Slicer3 module)
:* '''6. MRML scene creation'''
:** Creation of a MRML scene describing all the steps of the pipeline

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== Download ==

Executable and tutorial dataset: http://www.nitrc.org/projects/arctic/

Pediatric atlas: http://www.insight-journal.org/midas/item/view/2277

==Tutorials==

• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

Inputs: T1-weighted image, T1-weigthed atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/
--atlas Atlas.gipl --atlasParcellation Parcellation.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* ARCTIC source code (SVN, CVS) available to the community

File:ArcticLogo.png

2009-03-19T19:35:00Z

Mathieuc:

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-03-06T19:27:16Z

Mathieuc: /* Planning */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]
__NOTOC__

<center>
{|
|[[Image:Screenshot_Slicer.jpg|thumb|250px|Screenshot of the application]]
|valign="center"|[[Image:Schema_pipeline_ARCTIC.jpg|thumb|600px|Pipeline description]]
|}
</center>

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developped: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 module)

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== Download ==

Executable and tutorial dataset: http://www.nitrc.org/projects/arctic/

Pediatric atlas: http://www.insight-journal.org/midas/item/view/2277

==Tutorials==

• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

Inputs: T1-weighted image, T1-weigthed atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/
--atlas Atlas.gipl --atlasParcellation Parcellation.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"
:* Pediatric atlases available to the community through MIDAS
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3) and Tutorial dataset
:* New version including quality control through MRML scene, and WM, GM models generation

=== In progress ===
:* Comparison to FreeSurfer (180 cases dataset): pearson correlation analysis
:* ARCTIC source code (SVN, CVS) available to the community

DBP2:UNC:Regional Cortical Thickness Pipeline

2009-01-26T19:48:34Z

Mathieuc: /* Download */

Back to [[DBP2:UNC:Cortical_Thickness_Roadmap | UNC Cortical Thickness Roadmap]]
__NOTOC__

<center>
{|
|[[Image:Screenshot_Slicer.jpg|thumb|250px|Screenshot of the application]]
|valign="center"|[[Image:Schema_pipeline_ARCTIC.jpg|thumb|600px|Pipeline description]]
|}
</center>

== Objective ==

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.

This page describes the related pipeline with its basic components, as well as its validation.

== Pipeline overview ==

A Slicer3 high-level module for individual cortical thickness analysis has been developped: ARCTIC (Automatic Regional Cortical ThICkness)

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

:* '''1. Tissue segmentation'''
:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
:** Tool: itkEMS (UNC Slicer3 external module)
:* '''2. Regional atlas deformable registration'''
:** 2.1 Skull stripping using previously computed tissue segmentation label image
:*** Tool: SegPostProcess (UNC Slicer3 external module)
:** 2.2 T1-weighted atlas deformable registration
:*** B-spline pipeline registration
:*** Tool: RegisterImages (Slicer3 module)
:** 2.3. Applying transformation to the parcellation map
:*** Tool: ResampleVolume2 (Slicer3 module)
:* '''3. Cortical Thickness'''
:** Sparse asymmetric local cortical thickness
:** Tool: CortThick (UNC Slicer3 module)

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules.
The user can thus compute an individual regional cortical thickness analysis by running the 'ARCTIC' module, either within Slicer3 or as a command line.

== Download ==

Executable and tutorial dataset: http://www.nitrc.org/projects/arctic/

Pediatric atlas: http://www.insight-journal.org/midas/item/view/2277

==Tutorials==

• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

<center>
{|
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
|}
</center>

== ARCTIC (Automatic Regional Cortical ThICkness) usage: ==

=== Prerequities ===

Add directories to the PATH variable
-tcsh usage : setenv PATH ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
-bash usage : export PATH=ARCTIC-Executables-Directory:Slicer3D-Plugins-Directory:Batchmake-Directory:${PATH}
Notice : To execute ARCTIC within Slicer3D, it is not necessary to add "Slicer3D-Plugins-Directory" in the PATH.

Set an environment variable
-tcsh usage : setenv BatchmakeWrapper_Dir Batchmake-Wrapper-Directory
-bash usage : export BatchmakeWrapper_Dir=Batchmake-Wrapper-Directory

Set ARCTIC as a Slicer3D module
Within Slicer3D : View -> Applications Settings -> Module Settings -> Add a preset button and then select the ARCTIC-Executables-Directory/

=== Command line execution ===

Inputs: T1-weighted image, T1-weigthed atlas, regional atlas (parcellation map)

ARCTIC --T1 Image_T1.gipl --segAtlasDir TissueSegmentationAtlasDirectory/
--atlas Atlas.gipl --atlasParcellation Parcellation.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

=== Step by step command line execution ===

:* '''1. Tissue segmentation'''
:**Input: EMSparam.xml
:**Output: Image_Corrected_EMS.gipl, Label.gipl
itkEMSCLP --XMLFile EMSparam.xml
:* '''2. Skull stripping'''
:**Input: Label.gipl, Image_Corrected_EMS.gipl
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optional)
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS.gipl
:* '''3. Deformable registration of pediatric regional atlas'''
:**3.1 Deformable registration of T1-weighted pediatric atlas
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl
:***Output: Atlas_Registered.gipl, Atlas_Registered_Transform.txt
RegisterImages Image_Corrected_EMS_Stripped.gipl Atlas.gipl –resampledImage Atlas_Registered.gipl –saveTransform Atlas_Registered_Transform.txt –registration PipelineBSpline
:**3.2. Applying transformation to the parcellation map
:***Input: Parcellation.gipl, Atlas_Registered_Transform.txt, Image_Corrected_EMS_Stripped.gipl
:***Output: Parcellation_Registered.gipl
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Atlas_Registered_Transform.txt -i nn -R Image_Corrected_EMS_Stripped.gipl
:* '''4. Cortical Thickness'''
:**Input: Parcellation_Registered.gipl, Label.gipl
:**Output: CortThick_Result_Dir/, WMCorticalThicknessMap, GMCorticalThicknessMap
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --SaveWM WMCorticalThicknessMap --SaveGM GMCorticalThicknessMap

== Pipeline validation ==

=== Analysis on a small pediatric dataset ===

Tests have been computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
:* 16 autistic cases
:* 1 developmental delay
:* 3 normal control

=== Comparison to state of the art ===

We would like to compare our pipeline with FreeSurfer. We have thus started to perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.

Two distinct groups are considered: 2 year-old cases and 4 year-old cases.

== Planning ==

=== Done ===
:* Workflow for individual analysis (Slicer3 external module using BatchMake)
:* 2 Tutorials with application example on a small dataset : "How to use the UNC modules to compute the regional cortical thickness" and "How to use ARCTIC"

=== In progress ===
:* Pediatric atlases available to the community through MIDAS
:* Comparison to FreeSurfer: pearson correlation analysis
:* ARCTIC available to the community through NITRC: executables (UNC external modules for Slicer3), source code (SVN) and Tutorial dataset

=== Future work ===
:* Workflow for group analysis (KWWidgets application using BatchMake)

2009 Winter Project Week:RegionalCorticalThicknessPipeline

2009-01-09T16:58:34Z

Mathieuc:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Screenshot_Slicer.jpg|thumb|250px|Screenshot of the application]]
|valign="center"|[[Image:Schema_pipeline_ARCTIC.jpg|thumb|600px|Pipeline description]]
|}

__NOTOC__

===Key Investigators===
* UNC: Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett
* GE: Jim Miller

<div style="margin: 20px;">

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

<h1>Objective</h1>
We have developped an end-to-end application within Slicer3 allowing individual analysis of regional cortical thickness.
We are also developing an end-to-end application allowing group comparison.

Such a workflow applied to the young brain (2-4 years old) is our goal in order to start a longitudinal study of early brain development in [[DBP2:UNC|autism (UNC DBP)]].

See our [[DBP2:UNC:Cortical_Thickness_Roadmap| Roadmap]] for more details.
</div>

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

<h1>Approach, Plan</h1>

Our plan for the project week is to improve the integration of the regional cortical thickness module within Slicer:
*Specific directory within Slicer3 tree to store external modules available on NITRC
*Specific directory within Slicer3 tree to store batchmake xml description files (.bmm)

Meanwhile, we will continue to develop the KWWidgets application allowing group comparison.

</div>

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

<h1>Progress</h1>

During the week, a better integration of the module in Slicer3 was done.

We also worked on the quality control. A "mrml" scene is created at the end of the pipeline. This scene contains different Slicer3 snapshots representing the different steps. There is still a small bug with the mrml scene but it is close to be fixed.

</div>

<br style="clear: both;" />

</div>

===References===

2009 Winter Project Week:RegionalCorticalThicknessPipeline

2009-01-09T16:57:58Z

Mathieuc:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Screenshot_Slicer.jpg|thumb|250px|Screenshot of the application]]
|valign="center"|[[Image:Schema_pipeline_ARCTIC.jpg|thumb|600px|Pipeline description]]
|}

__NOTOC__

===Key Investigators===
* UNC: Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett
* GE: Jim Miller

<div style="margin: 20px;">

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

<h1>Objective</h1>
We have developped an end-to-end application within Slicer3 allowing individual analysis of regional cortical thickness.
We are also developing an end-to-end application allowing group comparison.

Such a workflow applied to the young brain (2-4 years old) is our goal in order to start a longitudinal study of early brain development in [[DBP2:UNC|autism (UNC DBP)]].

See our [[DBP2:UNC:Cortical_Thickness_Roadmap| Roadmap]] for more details.
</div>

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

<h1>Approach, Plan</h1>

Our plan for the project week is to improve the integration of the regional cortical thickness module within Slicer:
*Specific directory within Slicer3 tree to store external modules available on NITRC
*Specific directory within Slicer3 tree to store batchmake xml description files (.bmm)

Meanwhile, we will continue to develop the KWWidgets application allowing group comparison.

</div>

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

<h1>Progress</h1>

During the week, a better integration of the module in Slicer3 was done.
We also worked on the quality control. A "mrml" scene is created at the end of the pipeline. This scene contains different Slicer3 snapshots representing the different steps. There is still a small bug with the mrml scene but it is close to be fixed.

</div>

<br style="clear: both;" />

</div>

===References===

UNC ARCTIC Tutorial

2009-01-07T01:21:37Z

Mathieuc: /* Tutorials */

[[Image:Arctic_Logo.png |300px|thumb|right]]

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following those tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 in order to perform a regional cortical thickness analysis step by step.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorials==

• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' : UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

UNC ARCTIC Tutorial

2009-01-07T01:21:26Z

Mathieuc: /* Tutorials */

[[Image:Arctic_Logo.png |300px|thumb|right]]

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following those tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 in order to perform a regional cortical thickness analysis step by step.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorials==

• '''ARCTIC tutorial''' : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• '''UNC Modules tutorial''' :UNC Slicer3 modules to perform regional cortical thickness analysis step by step[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

UNC ARCTIC Tutorial

2009-01-07T01:19:53Z

Mathieuc: /* Tutorials */

[[Image:Arctic_Logo.png |300px|thumb|right]]

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following those tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 in order to perform a regional cortical thickness analysis step by step.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorials==

• ARCTIC tutorial (end-to-end Slicer3 module to perform automatic regional cortical thickness analysis)[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• UNC Modules tutorial (UNC Slicer3 modules to perform regional cortical thickness analysis step by step)[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

UNC ARCTIC Tutorial

2009-01-07T01:14:39Z

Mathieuc:

[[Image:Arctic_Logo.png |300px|thumb|right]]

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following those tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 in order to perform a regional cortical thickness analysis step by step.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorials==

• ARCTIC tutorial (end-to-end Slicer3 module)[[Media:ARCTIC-Slicer3-Tutorial.ppt|‏ [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ [pdf]]]

• UNC Modules tutorial (UNC modules to perform regional cortical thickness analysis)[[Media:UNC_Modules-Slicer3-Tutorial.ppt| [ppt]‏]][[Media:UNC_Modules-Slicer3-Tutorial.pdf| [pdf]‏]]

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

File:ARCTIC-Slicer3-Tutorial.pdf

2009-01-07T01:10:31Z

Mathieuc:

File:UNC Modules-Slicer3-Tutorial.pdf

2009-01-07T01:08:24Z

Mathieuc:

ARCTIC Tutorial

2009-01-07T01:02:27Z

Mathieuc: Removing all content from page

UNC ARCTIC Tutorial

2009-01-07T00:59:32Z

Mathieuc:

[[Image:Arctic_Logo.png |300px|thumb|right]]

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following those tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 in order to perform a regional cortical thickness analysis step by step.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorials==

• [[Media:ARCTIC-Slicer3-Tutorial.ppt|ARCTIC tutorial (end-to-end Slicer3 module)‏]]

• [[Media:UNC_Modules-Slicer3-Tutorial.ppt|UNC Modules tutorial (UNC modules to perform regional cortical thickness analysis)‏]]

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

UNC ARCTIC Tutorial

2009-01-07T00:53:54Z

Mathieuc:

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following those tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 in order to perform a regional cortical thickness analysis step by step.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorials==

• [[Media:ARCTIC-Slicer3-Tutorial.ppt|ARCTIC tutorial (end-to-end Slicer3 module)‏]]

• [[Media:UNC_Modules-Slicer3-Tutorial.ppt|UNC Modules tutorial (UNC modules to perform regional cortical thickness analysis)‏]]

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

UNC ARCTIC Tutorial

2009-01-07T00:48:04Z

Mathieuc: /* ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial */

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following thoss tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 in order to perform a regional cortical thickness analysis step by step.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorial==

• [http://www.nitrc.org/projects/arctic/ ARCTIC tutorial (end-to-end Slicer3 module)‏]

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

File:UNC Modules-Slicer3-Tutorial.ppt

2009-01-07T00:45:14Z

Mathieuc:

File:ARCTIC-Slicer3-Tutorial.ppt

2009-01-07T00:30:32Z

Mathieuc:

UNC ARCTIC Tutorial

2009-01-06T23:24:09Z

Mathieuc: /* Overview */

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following thoss tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 in order to perform a regional cortical thickness analysis step by step.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorial==

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

UNC ARCTIC Tutorial

2009-01-06T22:31:39Z

Mathieuc: /* Tutorial materials */

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following thoss tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 or using the command line.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorial==

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatric atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

UNC ARCTIC Tutorial

2009-01-06T22:20:18Z

Mathieuc: /* Overview */

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following thoss tutorials, you will be able to perform an individual analysis of regional cortical thickness.
In the ARCTIC tutorial, you will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.
And in the UNC external modules, you will be able to run the UNC external modules within Slicer3 or using the command line.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorial==

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatic atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

UNC ARCTIC Tutorial

2009-01-06T22:07:01Z

Mathieuc: New page: =ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial= ==Overview== Following this tutorial, you will be able to perform an individual analysis of regional cortical thickness....

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following this tutorial, you will be able to perform an individual analysis of regional cortical thickness.
You will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorial==

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatic atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett

Events:TutorialContestJan2009

2009-01-06T22:05:56Z

Mathieuc: /* Entries */

[[Image:Munich2008-Seb.jpg |250px|thumb|right]]
=Background=

[http://www.slicer.org Slicer3] is now being used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and functionality available in Slicer. Examples for such existing tutorials are the level 1 and 2 courses in the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training#Training_Compendium|NA-MIC training compendium].

<br>

=Tutorial Contest Goal=
The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups.
<br>
There will be two categories:
#'''END TO END SOLUTION TUTORIAL:''' In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. Entries into this category will require at least:
#*materials about the scientific and application background and motivation,
#*step-by-step guides, and
#*sample data
#*Example: [[IGT:ToolKit/Neurosurgical-Planning|Neurosurgical Planning for Image Guided Therapy using Slicer3]]
#'''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data. Entries into this category will require at least:
#*materials about the scientific and application background of the algorithm(s) and their use in the Slicer environment
#*step-by-step guides, and
#*at least two different sample data sets from two different institutions
#*Example: [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|Automatic Segmentation Tutorial using Slicer3]]
<br>

=Template=
A basic template has been used for all of the tutorials. The same design should be used for the contest. It can be found here: [[Media:TrainingTutorialTemplate.ppt|Template]]
*Note: The examples above predate the template.

=Rules=
*Tutorial must be based on a snapshot or release of Slicer 3
*Tutorial must follow the guidelines specified above
*If applicable, provide clear directions for downloading and installing additional modules
*The tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Applicants must agree to work with the NA-MIC Training and Dissemination Cores to curate their submission (we will test it on each of the available platforms and for usability and work with you to smooth any issues after the contest).
<br>

=Prizes=
Winning contestants from each category will receive a cash prize courtesy of Kitware Inc.
*1st: $250
*2nd: $150
*3rd: $100
<br>

=Dates=
*Submission: Tuesday, January 6th, Midnight, Utah time (MST) (there will be '''no extensions''')
*Review: Wednesday, January 7th
*Decisions announced: Thursday January 8th at NA-MIC All-Hands-Meeting
<br>

=Judges=
*Ron Kikinis
*Luis Ibanez
*Steve Pieper
*Randy Gollub
*Sonia Pujol
*Core 1 representative
<br>

=Questions=
Contact Training Core PI: Randy L. Gollub (rgollub at partners dot org)
<br>

=Entries=
#[[Iowa Meshing Tutorial]] - Demonstrates the new hexahedral meshing capabilities Slicer3 using a proximal phalanx bone
#[[Non-human Primates Segmentation Tutorial]] - Virginia Tech - Demonstrates how to use Slicer3 for skull stripping and automatically segmenting non-human primate MR images.
#[[IGT:ToolKit/Prostate-Planning|Prostate Therapy Planning Tutorial]] - Demonstrates how to use Slicer3 for MRI-guided prostate interventions, including clinical background, B-spline registration, manual segmentation and model making
#[[IGT:ToolKit/Navigation-tutorial|Basic Slicer3 Navigation Tutorial]] - Demonstration of navigation using OpenIGTLink, using a tracking simulator
#[[Python Stochastic Tractography Tutorial]] - Demonstrates the new stochastic tractography module of Slicer3 using a DWI image and a region of interest.
#[[UNC ARCTIC Tutorial]] - Demonstrates how to use ARCTIC to perform a regional cortical thickness analysis within Slicer3.

ARCTIC Tutorial

2009-01-06T22:02:29Z

Mathieuc: /* Softwares */

[[Image:Arctic_Logo.png|300px|thumb]]

=ARCTIC (Automatic Regional Cortical ThICkness) Slicer3 Tutorial=

==Overview==

Following this tutorial, you will be able to perform an individual analysis of regional cortical thickness.
You will learn how to load input volumes, run the end-to-end module ARCTIC to generate cortical thickness information and display output volumes.

Roadmap project : http://www.na-mic.org/Wiki/index.php/DBP2:UNC:Regional_Cortical_Thickness_Pipeline

==Tutorial==

==Software==
• Slicer3
http://www.slicer.org/pages/Downloads

• BatchMake‏
http://www.batchmake.org/batchmake/resources/software.html

==Tutorial materials==
• [http://www.nitrc.org/projects/arctic/ BatchMake wrapper (ARCTIC_BatchMake_Wrapper_1.0)‏]

• [http://www.nitrc.org/projects/arctic/ Tutorial dataset(ARCTIC_Tutorial_example_1.0)]‏

• [http://www.nitrc.org/projects/arctic/ External modules (ARCTIC_Executables_1.0)]

• [http://www.insight-journal.org/midas/item/view/2277 ‏Pediatic atlas (UNC_Pediatric_Brain_Atlas)]‏

==People==
Cedric Mathieu

Clement Vachet

Martin Styner

Heather Cody Hazlett