Created
May 23, 2019 13:51
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datalad rev-create hirni-bids | |
cd hirni-bids | |
datalad run-procedure setup_hirni_dataset | |
## import dicom recently tarred off the dicom server | |
datalad hirni-import-dcm -d . ../PD00020_05122018.tar.gz acq001 | |
## confirm the subdataset has been created | |
datalad subdatasets | |
cd acq001/dicom | |
# check whether extractor is active on dataset | |
git config -f .datalad/config -l | |
# if it's not there, add dicom extractor | |
git config -f .datalad/config --add datalad.metadata.nativetype dicom | |
# confirm it's added | |
git config -f .datalad/config -l | |
# aggregate metadata on subdataset | |
datalad aggregate-metadata --force-extraction -d . -r --update-mode all | |
# go back up to parent | |
cd ../.. | |
# check whether extractor is active on dataset | |
git config -f .datalad/config -l | |
# if it's not there, add dicom extractor | |
git config -f .datalad/config --add datalad.metadata.nativetype dicom | |
##git config -f .datalad/config --add datalad.metadata.nativetype bids | |
##git config -f .datalad/config --add datalad.metadata.nativetype nifti1 | |
# confirm it's there | |
git config -f .datalad/config -l | |
## aggregate metadata, percolate up | |
datalad aggregate-metadata --force-extraction -d . -r --update-mode all | |
## prepare for bids conversion | |
datalad run-procedure setup_bids_dataset | |
## generate spec from dicom metadata | |
datalad hirni-dicom2spec -d acq001/dicoms -s studyspec2.json acq001/dicoms | |
## perform bids conversion based on spec | |
datalad hirni-spec2bids -d . sourcedata/studyspec2.json |
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So, I'd take everything until line 28 and make this
hirni_raw
instead.For the actual BIDS I'd suggest to have separate dataset: