This code takes input structural MRI nifti(.nii) files in BIDS format and runs Voxel Based Morphometry(VBM) on them. The outputs are Registered (to SPM template)segmented images (wc1.niii-white matter, wc2*.nii-gray matter, wc3*.nii-cerebro spinal fluid)
Docker image which has all the dependencies, link to docker hub will be updated soon.
run the script run_vbm_bids.py and pass two command line arguments 1st arg-Path to BIDS directory , where the script can find structural MRI nii files for various subjects 2nd arg-Temperary path where the output should be written to
EX: python3 "/data/scripts/process_bids/run_vbm_bids.py" '/data/scripts/process_bids/bids_input' '/data/scripts/process_bids/bids_output'