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:

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

7. 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

8. 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:

• FSL (https://fsl.fmrib.ox.ac.uk/fsl)
• SPM12 (https://www.fil.ion.ucl.ac.uk/spm/software/spm12/)
• NODDI toolbox (http://mig.cs.ucl.ac.uk/index.php?n=Tutorial.NODDImatlab)
• VSK - *3 functions are modified (http://coewww.rutgers.edu/www2/vizlab/liliu/research/skeleton/VSK)
• splinefit (https://www.mathworks.com/matlabcentral/fileexchange/13812-splinefit)
• PALM (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM)
• NaN (http://pub.ist.ac.at/~schloegl/matlab/NaN/)
• Gramm (https://www.mathworks.com/matlabcentral/fileexchange/54465-gramm-complete-data-visualization-toolbox-ggplot2-r-like)
• Shaded Error Bar (https://www.mathworks.com/matlabcentral/fileexchange/26311-raacampbell-shadederrorbar)

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