Difference between revisions of "DBP2:UNC:Regional Cortical Thickness Pipeline"
From NAMIC Wiki
Line 12: | Line 12: | ||
Input: T1-weighted image | Input: T1-weighted image | ||
− | :* 1. Tissue segmentation | + | :* '''1. Tissue segmentation''' |
:** Tool: itkEMS (UNC Slicer3 external module) | :** Tool: itkEMS (UNC Slicer3 external module) | ||
− | :* 2. Skull stripping | + | :* '''2. Skull stripping''' |
:** Tool: SegPostProcess (UNC Slicer3 external module) | :** Tool: SegPostProcess (UNC Slicer3 external module) | ||
− | :* 3. Deformable registration of pediatric regional atlas | + | :* '''3. Deformable registration of pediatric regional atlas''' |
:** 3.1 Deformable registration of T1-weighted pediatric atlas | :** 3.1 Deformable registration of T1-weighted pediatric atlas | ||
:***Tool: RegisterImages (Slicer3 module) | :***Tool: RegisterImages (Slicer3 module) | ||
:** 3.2. Applying transformation to the parcellation map | :** 3.2. Applying transformation to the parcellation map | ||
:*** Tool: ResampleVolume2 (Slicer3 module) | :*** Tool: ResampleVolume2 (Slicer3 module) | ||
− | :* 4. Cortical Thickness | + | :* '''4. Cortical Thickness''' |
:** Tool: CortThick (UNC Slicer3 module) | :** Tool: CortThick (UNC Slicer3 module) | ||
Line 33: | Line 33: | ||
Input regional atlas (parcellation map): | Input regional atlas (parcellation map): | ||
− | :* 1. Tissue segmentation | + | :* '''1. Tissue segmentation''' |
:**Input: EMSparam.xml | :**Input: EMSparam.xml | ||
:**Output: Image_Corrected_EMS.gipl, Label.gipl | :**Output: Image_Corrected_EMS.gipl, Label.gipl | ||
itkEMSCLP EMSparam.xml | itkEMSCLP EMSparam.xml | ||
− | :* 2. Skull stripping | + | :* '''2. Skull stripping''' |
:**Input: Label.gipl, Image_Corrected_EMS.gipl | :**Input: Label.gipl, Image_Corrected_EMS.gipl | ||
:**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optionnal) | :**Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optionnal) | ||
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS_Stripped.gipl (--mask BinaryMask.gipl –dilate) | SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS_Stripped.gipl (--mask BinaryMask.gipl –dilate) | ||
− | :* 3. Deformable registration of pediatric regional atlas | + | :* '''3. Deformable registration of pediatric regional atlas''' |
:** 3.1 Deformable registration of T1-weighted pediatric atlas | :** 3.1 Deformable registration of T1-weighted pediatric atlas | ||
:***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl | :***Input: Atlas.gipl, Image_Corrected_EMS_Stripped.gipl | ||
Line 50: | Line 50: | ||
:***Output: Parcellation_Registered.gipl | :***Output: Parcellation_Registered.gipl | ||
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Parcellation_Registered.gipl -i nn -R Image_Corrected_EMS_Stripped.gipl | ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Parcellation_Registered.gipl -i nn -R Image_Corrected_EMS_Stripped.gipl | ||
− | :* 4. Cortical Thickness | + | :* '''4. Cortical Thickness''' |
:**Input: Parcellation_Registered.gipl, Label.gipl | :**Input: Parcellation_Registered.gipl, Label.gipl | ||
:**Output: CortThick_Result_Dir/ | :**Output: CortThick_Result_Dir/ |
Revision as of 22:29, 12 August 2008
Home < DBP2:UNC:Regional Cortical Thickness PipelineBack to UNC Cortical Thickness Roadmap
Objective
We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.
General information
Pipeline description (steps)
Input: T1-weighted image
- 1. Tissue segmentation
- Tool: itkEMS (UNC Slicer3 external module)
- 2. Skull stripping
- Tool: SegPostProcess (UNC Slicer3 external module)
- 3. Deformable registration of pediatric regional atlas
- 3.1 Deformable registration of T1-weighted pediatric atlas
- Tool: RegisterImages (Slicer3 module)
- 3.2. Applying transformation to the parcellation map
- Tool: ResampleVolume2 (Slicer3 module)
- 3.1 Deformable registration of T1-weighted pediatric atlas
- 4. Cortical Thickness
- Tool: CortThick (UNC Slicer3 module)
- 1. Tissue segmentation
All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules. The user can thus compute a regional cortical thickness analysis on one data, either within Slicer3 or by running the tools as command lines.
Usage (Command Line)
Input T1_weighted image: Input T1-weigthed atlas: Input regional atlas (parcellation map):
- 1. Tissue segmentation
- Input: EMSparam.xml
- Output: Image_Corrected_EMS.gipl, Label.gipl
- 1. Tissue segmentation
itkEMSCLP EMSparam.xml
- 2. Skull stripping
- Input: Label.gipl, Image_Corrected_EMS.gipl
- Output: Image_Corrected_EMS_Stripped.gipl, BinaryMask.gipl (optionnal)
- 2. Skull stripping
SegPostProcessCLP Label.gipl Image_Corrected_EMS_Stripped.gipl --skullstripping Image_Corrected_EMS_Stripped.gipl (--mask BinaryMask.gipl –dilate)
- 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
- 3.1 Deformable registration of T1-weighted pediatric atlas
- 3. Deformable registration of pediatric regional atlas
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
- 3.2. Applying transformation to the parcellation map
ResampleVolume2 Parcellation.gipl Parcellation_Registered.gipl -f Parcellation_Registered.gipl -i nn -R Image_Corrected_EMS_Stripped.gipl
- 4. Cortical Thickness
- Input: Parcellation_Registered.gipl, Label.gipl
- Output: CortThick_Result_Dir/
- 4. Cortical Thickness
CortThickCLP CortThick_Result_Dir/ --par Parcellation_Registered.gipl --inputSeg Label.gipl --Wm --Gm --Vtk --Sdm –BvsI --GMMaps
Analysis on a small pediatric dataset
Tests have been computed on a small pediatric dataset, including 2 years old and 4 years old cases
- 2 Autistic cases
- 1 developmental delay
- 1 normal control
In progress
- Workflow for individual analysis (Slicer3 external module using BatchMake)
Future work
- UNC Slicer3 external modules available on NITRIC
- Pediatric atlas (T1-weighted image and parcellation map) available to the community (XNAT?)
- Workflow for group analysis