I have dcm2bids installed, and I want to use it on my own data to start. The data is a set of .tgz files in one directory.
I wrote a config.json file in what looks like the appropriate way; it loads when I run (following a tutorial I followed here; BIDS Overview and Tutorial — Andy's Brain Book 1.0 documentation):
dcm2bids_scaffold -o BIDS/bidsout
dcm2bids -d PilotStudy/PilotSession11/data/dicoms -p 01 -c BIDS/BIDS_config_p11.json -o BIDS/bidsout --forceDcm2niix
but then dcm2bids fails because:
INFO:dcm2bids.dcm2bids:BIDS directory: /Volumes/vision/Data/BIDS/bidsout
INFO:dcm2bids.utils:Running ['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', PosixPath('BIDS/bidsout/tmp_dcm2bids/sub-01'), PosixPath('PilotStudy/PilotSession11/data/dicoms')]
Error: Unable to find any DICOM images in PilotStudy/PilotSession11/data/dicoms (or subfolders 5 deep)
But that is the directory with the data. Am I not formatting the command correctly? Surely I don’t have to pre-extract the dcms from each tgz (i have used dcm2niix from within matlab and python packages and pointing it at tgz files works - is that some extra capability of other packages?)… Or…?
Thanks!
-andrew