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ROI
 
 
 
 
 
 
 
 
 
 

This repository contains the codes created or used for the analysis in the paper "Cognitive and White-Matter Compartment Models Reveal Selective Relations between Corticospinal Tract Microstructure and Simple Reaction Time"

DOI: https://doi.org/10.1523/JNEUROSCI.2954-18.2019

For more information on the codes, please contact: esin.karahan@gmail.com

web: https://ccbrain.org/

The pipeline is shown as:

pipeline

Following steps correspond to the order in the pipeline. All MATLAB functions and bash scripts are provided.

  1. Preprocessing of DWI files

    FSL tools (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide)

  2. DTI tensor fitting

    FSL tools (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide)

  3. NODDI fitting

    NODDI toolbox (http://mig.cs.ucl.ac.uk/index.php?n=Tutorial.NODDImatlab)

  4. Probabilistic Tractography

    FSL tools (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#PROBTRACKX_-_probabilistic_tracking_with_crossing_fibres)

    • Seed, waypoint and target masks to generate Corticospinal tracts, Optic radiations and Cingulum Bundles are given in the ROI folder. The scripts to generate subject-soecific ROIs are given in the Bash folder.
  5. Group mask

    • call_createGroupProbImage.m
    • createGroupProbImage.m
  6. Skeletonization ./Skeleton director

  • Main_tractSkeleton.m

    • removeVoxel.m
    • pruneBranchSkel.m
    • organizeSkelLine.m
    • spline3dCurveInterpolation.m
    • limitSkelwithImage.m
    • divideSkel.m
    • assignVoxel2Skeleton.m
  • VSK toolbox (http://coewww.rutgers.edu/www2/vizlab/liliu/research/skeleton/VSK)

    additional functions for the VSK

    • findFirstandLastPointsTract.m
    • findBoxVolume.m
    • findImageCenter.m

    modified functions of the VSK

    • skel_Distmethod_mod.m
    • skel_thinningmethod_mod.m
  • resampleSkeleton.m

    • bordersWayPointROI_CST.m
    • divideSkelOverlap.m
    • assignVoxel2SkeletonOverlap.m
    • writeLabelImageOverlap.m
    • euclideanDist3.m
  • Visualization functions

    • visualizeObject.m
    • visualizeObjectSkel.m
  1. Individual Mapping of DTI and NODDI metrics ./TractStat Directory
  • Erode the FA maps

    tbss_1_preproc (FSL)

  • Create WM masks from T1 images of subjects and register to native DWI space (b0) so that the FA and MD can be masked.

    • segment_T1.sh
    • register_WM_to_b0.sh
  • Register the tracts (fdt) back to the native DWI space

    • register_fdt_to_b0.sh
  • Main_tractSkeletonStatFA.m

  • Main_tractSkeletonStatNODDI.m

    • averageFAMDtractSkeletonOverlapReg.m
    • saveAlongTractMetrixTxt.m
    • plotMetricsAlongTract.m
  • Main_tractSkeletonStatWholeTract.m

    • averagetract.m
  1. Statistics ./TractStat Directory
  • statFunctList
    • statPalmImageCluster_CSV_TFCE.m

    • statPalmImageCluster_findSignificant.m

      • plotRegTract.m
    • statMapCorrSkel2GroupIm.m

      Note that: Any image viewer can be used to visualize the significant segments of the tracts - findIgnoranceColumns.m

-Partial Correlation on the whole tract

  • statPartialCorrWholeTract.m

Dependency on other toolboxes:

Auxiliary functions:

  • takemeanNan.m
  • takesemNan.m
  • bootciMeanNan.m

Change the following files according to your environment:

  • Set the root path in 'setDirectory.m'
  • Run setEnvironment.m
  • Run call_createGroupProbImage

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Along Tract Analysis of DWI

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