DTI Processing Pipeline with Distortion Correction and LE patching

The processing pipeline to perform distortion correction and Leukoencephalopathy (LE) patching for DTI structure connectome

Prerequisites

-Installed FSL 6.
-Installed MRTrix3.
-Installed ANTs.

The scripts use following files:
DWI files in dcm format under folder name included DTI
brain.mgz : an extracted brain image generated by freesurfer.
hcpmmp1.mgz and aparc+aseg.mgz.

Scripts

mrtrixdistcorr_pipeline.sh is the main script.

Usage:

1. mrtrixdistcorr_pipeline.sh ProjDir MRN ExamDate TimePoint LE(0 or 1) THREADS
   assuming the path is
   ProjDir/MRN-TimePoint/DWI
   LE patching (yes 1, no 0)
   THREADS: number of threads used in the calcualtion

2. T1toT2.sh covert T1w image to T2w image
   T1toT2.sh $1(brain skull removed) $2 (output) $3 (TI value) $4 TE $5 (coreg? 0 no, 1 yes)

3. patch_T1_new.sh patch LE hypointensive T1w image or not.
   patch_T1_new.sh $1(input T1 image) $2(output, patched T1 image)

4. antsDWIReg.sh ANTs registration DWI to pseudo T2 image

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The scripts are for research use purpose only without any kind of warranty. Use at your own risk.