Summary of what happened:
Hey neurostars community!
I’m trying to use external atlases with XCP-D by following these steps: Running XCP-D — xcp_d 0.10.0rc4.dev5+g7694faa documentation
I’ve setup some external atlases, but I’m getting an error that suggests XCP-D won’t recognize them.
My external atlases are setup like so:
${HOME}/atlases/
SchaeferMSAMDTB10/
dataset_description.json
atlas-Schaefer4007MSA4MDTB10/
atlas-Schaefer4007MSA4MDTB10_dseg.json
atlas-Schaefer4007MSA4MDTB10_dseg.tsv
atlas-Schaefer4007MSA4MDTB10_space-MNI152NLin6Asym_res-01_dseg.nii.gz
atlas-Schaefer4007MSA4MDTB10_space-MNI152NLin2009cAsym_res-01_dseg.nii.gz
dataset_description.json includes:
{"BIDSVersion": "1.8.0", "DatasetType": "atlas"}
atlas-Schaefer4007MSA4MDTB10_dseg.json includes:
{"BIDSVersion": "1.8.0", "Name": "Schaefer4007MSA4MDTB10"}
atlas-Schaefer4007MSA4MDTB10_dseg.tsv includes “index” and “label” columns (amongst some other columns).
However, seems my atlases just aren’t being recognized, but I’m not sure what I’m doing wrong. Thanks!
Command used (and if a helper script was used, a link to the helper script or the command generated):
My xcp-d call:
docker run --rm -it --cpus=${NPROC} --memory=${MEMORY}GB \
-v ${FMRIPREP_DIR}:/fmriprep:ro \
-v ${XCPD_DIR}/wkdir:/work:rw \
-v ${XCPD_DIR}:/out:rw \
-v ${FREESURFER_HOME}:/freesurfer:ro \
-v ${HOME}/atlases:/atlases:ro \
pennlinc/xcp_d:0.9.1 \
/fmriprep /out participant \
--mode linc -w /work --input-type fmriprep --nuisance-regressors 36P --task_id rest \
--participant-label ${SUBJECT_ID_SHORT} \
--datasets myatl=/atlases/SchaeferMSAMDTB10 --atlases Schaefer4007MSA4MDTB10 \
--fs-license-file /freesurfer/license.txt \
--file-format nifti --nthreads ${NPROC} --low-mem --mem-gb ${MEMORY}
Version:
0.9.1
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
When I run this call, I get the following error:
xcp_d: error: argument --atlases: invalid choice: 'Schaefer4007MSA4MDTB10' (choose from '4S1056Parcels', '4S156Parcels', '4S256Parcels', '4S356Parcels', '4S456Parcels', '4S556Parcels', '4S656Parcels', '4S756Parcels', '4S856Parcels', '4S956Parcels', 'Glasser', 'Gordon', 'HCP', 'MIDB', 'MyersLabonte', 'Tian')