Difference between revisions of "DBP2:UNC:Regional Cortical Thickness Pipeline"

From NAMIC Wiki
Jump to: navigation, search
Line 4: Line 4:
 
<center>
 
<center>
 
{|
 
{|
−
|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
+
|[[Image:Screenshot_Slicer.jpg|thumb|250px|Screenshot of the application]]
−
|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
+
|valign="center"|[[Image:Schema_pipeline.jpg|thumb|600px|Pipeline description]]
−
|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
 
−
|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
 
 
|}
 
|}
 
</center>
 
</center>
Line 69: Line 67:
 
:* 1 normal control
 
:* 1 normal control
  
 +
<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>
  
 
=== In progress ===
 
=== In progress ===

Revision as of 20:32, 17 October 2008

Home < DBP2:UNC:Regional Cortical Thickness Pipeline

Back to UNC Cortical Thickness Roadmap


Screenshot of the application
Pipeline description

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, T2-weighted image, PD-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)
  • 4. 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 a regional cortical thickness analysis on one data, either within Slicer3 or by running the tools as command lines.

Usage (Command Line)

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

  • 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 (--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
  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

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
T1-weighted skull-stripped image
Parcellation image
Cortical thickness on WM surface
Cortical thickness information

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
Retrieved from "https://www.na-mic.org/w/index.php?title=DBP2:UNC:Regional_Cortical_Thickness_Pipeline&oldid=31135"