README.md

ke-berkeley

Pipeline to process DWI data. This pipeline assumes that DWI scans are centered at C6 vertebral levels.

Requirements

This pipeline was tested with SCT v4.2.2.

The dataset should be organized according to BIDS structure:

DATA/
└── data/
    └── sub-01
        |── anat
        |   └── sub-01_T2w.nii.gz
        |   └── sub-01_T2w.json
        |   └── sub-01_survey.nii.gz
        |   └── sub-01_survey.json
        └── dwi
            └── sub-01_dwi.nii.gz
            └── sub-01_dwi.json
            └── sub-01_dwi.bval
            └── sub-01_dwi.bvec

Installation

Clone this repository

git clone https://github.com/sct-pipeline/ke-berkeley.git
cd ke-berkeley
PATH_REPOS=`pwd`

Copy the file parameters.sh in the folder DATA/

How to run

Go to DATA/ folder and run:

sct_run_batch parameters.sh $PATH_REPOS/process_data.sh

The pipeline outputs:

• DATA/log/: Log files for each subject
• DATA/qc/: QC report
• DATA/results/: Result folder with all processed data and quantitative results.