custom_bids

custom bids conversion script utilizing python

assumes that you have installed dcm2niix and dcm2bids

conda install -c conda-forge dcm2niix

pip install dcm2bids

also assumes that you have all of the config files in the dicom folder

CCX_dcm/ccx_ses-1.json

CCX_dcm/ccx_ses-2.json

CCX_dcm/ccx_ses-3.json

CCX_dcm/ccx_ses-3-pre-10.json

CCX_dcm/ccx_nda.json

to run:

navigate terminal to the directory one level above the dicom folder

current_dir/CCX_dcm

initialize output folder by running:

python custom_bids.py -i True -o CCX-bids

convert a single subject by replacing CCX000 with the desired subject and running:

python custom_bids.py -s CCX000 -d CCX_dcm -o CCX-bids

display help:

python custom_bids.py --help

written gus hennings