Qiyu815/DTI-Scripts

A selection of scripts for DTI analysis with FSL

DTI-Scripts

A selection of scripts to guide and automate DTI analysis with FSL

Tools:

• Osirix – organize data
• Dcm2niix – convert dicom to nifti
  • from: https://github.com/rordenlab/dcm2niix
  • needs to be installed and added to path
• FSL – analyze data

Steps

0. Clone this repository into your workinng directory

   • type git clone https://github.com/MonsieurWave/DTI-Scripts into your terminal

1. Extract nifti, bvals and bvecs from dicoms:

   • Use the dcm2niix command line tool on dicom folder
   • place example.nii, example.bval and example.bvec in this subject's folder
   • Rename output to exampleSubject.nii, exampleSubject.bval and exampleSubject.bvec (or however your subject is named)

2. Organize your study directory:

   • Subject data should be in subject folder (ex: /Ana/subject1)
   • The subject folder and the subject's data should have the same name
   • Bvals, Bvecs and .nii files should be in every subject's folder (ex: /Ana/subject1/subject1.nii)

3. Compute DTI

   • Open the DTI_Computation.sh file
   • Modify the line 'subjs="subj01 subj02"' to list your subjects (ex: subjs="subject1 subject2 subject3")
   • Modify the line 'main_dir="/your/path/to/main/directory"' to point to the study directory (ex: main_dir="/Users/example/Ana")
   • Copy Paste the modified script into your terminal and run it (this might take some time)

4. View DTI images

   • Use fsleyes to view the computed images

5. ROI Data Extraction

   • Open the singleSubROI.sh file in ROI_Analysis/singleSubject/automaticROI
   • Modify the line 'subjs="subj01"' to match to your subject
   • Modify the line main_dir="/your/path/to/main/directory" to match your study directory
   • Modify the line ROIname="n8_R" to match your ROI
   • In fsleyes, identify the coordinates of your ROI and enter them into the singleSubROI.sh
   • Copy the first part (until the checkpoint) into your editor and execute it - a window will open
   • Verify the position of the ROI.
   • If it is correctly place, copy paste the rest of the file in your terminal and execute it. Otherwise repeat from start and change coordinates.
   • Data is saved in Analysis/Analysis.txt