Along Tract Analysis of DWI
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Skeleton
TractStat
auxiliaryFunctions
bash
README.md
call_createGroupProbImage.m
createGroupProbTractImage.m
pipelineTractVolSkel.png
readSubjectsFromFile.m
setDefinition.m
setDirectory.m
setEnvironment.m

README.md

This repository contains the codes created or used for the analysis in the paper (under preperation) "White matter microstructure along the primary motor and sensory pathways contribute to reaction speed variations in humans"

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)

  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