/inspiredsct

Spinal cord analysis scripts based on SCT

Primary LanguageShellMIT LicenseMIT

inspiredsct

Spinal cord analysis scripts based on SCT

File structure

data
  |- 001/
  |- 002/
  |- 003/
      |- bl/
	  |- brain/
    	  |- cord/
      	      |- dwi.nii.gz + bvals/bvecs
      	      |- t1_sag.nii.gz
      	      |- t2_sag.nii.gz
      	      |- t2_tra.nii.gz
      	      |- pd_medic.nii.gz
      	      |- processing_sct/
      	          |- t2/  # processing of t2_tra 
      	          |- t2s/  # processing of pd_medic
      	          |- dwi/  # processing of dwi

Getting started

  • Edit parameters.sh according to your needs.
  • Prepare data: ./run_process.sh prepare_data.sh
  • Process data: ./run_process.sh process_data.sh
  • Compute metrics: ./run_process.sh compute_metrics.sh

SCT version

This pipeline has been tested on SCT v3.1.1: https://github.com/neuropoly/spinalcordtoolbox/releases/tag/v3.1.1