arctic:MainPage

From NITRC Wiki

ARCTIC Logo

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

Executables and tutorial dataset

Available on NITRC : http://www.nitrc.org/projects/arctic/

ARCTIC is now directly available via | Slicer3 extension manager.

Release source code via svn

Required software/libraries

- Slicer Nighly Build

Download and install ARCTIC

Create and go to a ARCTIC/ directory

 mkdir ARCTIC
 cd ARCTIC

Download ARCTIC via svn :

 svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC

Create and go to a ARCTIC-build/ directory

 mkdir ARCTIC-build
 cd ARCTIC-build

Start the project configuration with ccmake

 ccmake ../ARCTIC

Configure the project

 Press 'c' to start the configuration, Press "e" to exit help
 Set "CMAKE_BUILD_TYPE" -> RelWithDebInfo
 Set "Slicer3_DIR" -> "your Slicer3-nightly_build"/lib/Slicer3
 Press "c" to configure, Press "g" to generate the Makefile

Compile ARCTIC

 make

CVS source code (within UNC NeuroLib)

Required software/libraries

Install required software to compile the NeuroLib

- CMake

- BatchMake (v 1.0.8 needed, use cvs access)

- FLTK

- Slicer Nighly Build

- Insight Application

Download and install the NeuroLib

Create and go to a NeuroLib/ directory

 mkdir NeuroLib
 cd NeuroLib

Download the NeuroLib with cvs :

 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 project configuration with ccmake

 ccmake ../NeuroLib

Configure the project

 Set ARCTIC at "ON"
 Press 'c' to start the configuration
 Set "CMAKE_BUILD_TYPE" -> RelWithDebInfo
 Set "COMPILE_ARCTIC" -> ON
 Press "c" to configure, Press "e" to exit help
 Set "VTK_DIR" -> "SLicer-nighly-build"/lib/vtk-5-2
 Press "c" to configure, Press "e" to exit help
 Set "ITK_DIR" -> "SLicer-nighly-build"/lib/InsightToolkit
 Press "c" to configure, Press "e" to exit help
 Set "FLTK_DIR" -> "your_FLTK-build_path"
 Set "FLTK_CONFIG_SCRIPT" -> "your_FLTK-build_path"/fltk-config
 Set "GENERATECLP_DIR" -> "SLicer-nighly-build"/lib/GenerateCLP
 Press "c" to configure, Press "e" to exit help
 Set "BATCHMAKE_DIR" -> "your_BatchMake-build_path"
 Press "c" to configure, Press "e" to exit help
 Set "INSIGHT_APPLICATIONS_BINARY_PATH" -> "your_InsightApplications-build_path"
 Set "BUILD_SHARED_LIB" -> OFF
 Press "c" to configure, Press "e" to exit help
 Press "g" to generate the makefile

Compile ARCTIC

 make

Complementary Downloads

Tutorials

• ‏ ARCTIC tutorial : end-to-end Slicer3 module to perform automatic regional cortical thickness analysis

Previous versions : ‏ [v1.0]‏ [v1.1]

• UNC Modules tutorial : UNC Slicer3 modules to perform regional cortical thickness analysis step by step

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}

Add libraries to the LD_LIBRARY_PATH variable

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

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 run 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
 --segAtlasOrientation : if the orientation of your tissue segmentation atlas is different than the default value (RAI), add this flag to set the right orientation
 --atlasOrientation : if the orientation of your atlas/parcellation 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 your 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
 --rawImageOrientation : if the orientation of your raw iamge is different than the default value (RAI), add this flag to set the right orientation
 --atlasOrientation : if the orientation of your atlas/parcellation is different than the default value (RAI), add this flag to set the right orientation
 --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

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ARCTIC

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arctic:MainPage

From NITRC Wiki

Contents

Objective

Pipeline overview

ARCTIC Download

Executables and tutorial dataset

Release source code via svn

Required software/libraries

Download and install ARCTIC

CVS source code (within UNC NeuroLib)

Required software/libraries

Download and install the NeuroLib

Complementary Downloads

Pediatric atlas

Adult atlas

Elderly atlas

Tutorials

ARCTIC (Automatic Regional Cortical ThICkness) usage:

Prerequities

Command line execution

Raw Image Mode

Segmented Image Mode

Step by step command line execution

Search

Toolbox