Summary of what happened:
I am running xcp-d on my fmriprep output. My data is structured so each subject has two sessions but only the first session has a anatomical scan. xcp-d produced an error saying it requires a one-to-one or one-to-all mapping between anatomical and functional sessions.
EDIT: fMRIPrep was run on both sessions and only creates an anat folder in first session folder. I should also clarify that this is not a longitudinal study and scans are collected within a week of each other.
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv \
-B /code/freesurfer/ \
${singularityDir}/xcp_d.sif \
${prepDir} ${xcpDir} participant --participant-label $SUBJECT \
--mode none \
--file-format nifti \
--despike n \
--fd-thresh 0.5 \
--input-type fmriprep \
--abcc-qc y \
--dummy-scans auto \
--lower-bpf 0.008 \
--upper-bpf 0.08 \
--smoothing 6 \
--linc-qc y \
--combine-runs n \
--motion-filter-type none \
--output-type censored \
--min-coverage 0.5 \
--warp-surfaces-native2std n \
-t rest \
-p 36P \
-w ${WDIR} \
--fs-license-file /code/freesurfer/license.txt \
--resource-monitor
Version:
0.11.0
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Relevant log outputs (up to 20 lines):
Atlas 'MIDB' requires CIFTI processing. Skipping atlas.
Atlas 'MyersLabonte' requires CIFTI processing. Skipping atlas.
Traceback (most recent call last):
File "/usr/local/miniconda/bin/xcp_d", line 8, in <module>
sys.exit(main())
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/run.py", line 25, in main
parse_args(args=sys.argv[1:])
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/parser.py", line 971, in parse_args
raise ValueError(
ValueError: XCP-D expects a one-to-one mapping between anatomical sessions and functional sessions, or a one-to-all mapping. Found 1 functional sessions that do not have anatomical data: 02