Summary of what happened:
I have preprocessed some multi-band multi-echo fMRI data with BIDS, including the --cifti-output flag.
I tried running XCP-D on the cifti outputs, but encountered an error saying that the --cifti flag is not recognized. I also tried the -s flag, but that failed as well.
Command used (and if a helper script was used, a link to the helper script or the command generated):
SUBJECT="001"
OUTPUT_SPACES="MNI152NLin2009cAsym anat fsnative"
$BIDS_PATH=/Path/To/My/Dataset
$LAB_SHARED=/Path/To/My/Singularity/Images
singularity run --cleanenv --bind $BIDS_PATH "${LAB_SHARED}/singularity_images/xcp_d-0.7.0.simg" \
${BIDS_PATH}derivatives \
${BIDS_PATH}/derivatives/xcp_d_070_acompcor_withtedana_ortho \
participant \
-w ${BIDS_PATH}/derivatives/xcpd_work \
--participant_label "${SUBJECT}" \
--nuisance-regressors acompcor \
--cifti
Version:
0.7.0 (also tested with 0.6.0)
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
Yes, BIDS.
Relevant log outputs (up to 20 lines):
usage: xcp_d [-h] [--version]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[-t TASK_ID] [--bids-filter-file FILE] [-s] [--nthreads NTHREADS]
[--omp-nthreads OMP_NTHREADS] [--mem_gb MEM_GB]
[--use-plugin USE_PLUGIN] [-v]
[--input-type {fmriprep,dcan,hcp,nibabies,ukb}]
[--dummy-scans {{auto,INT}}] [--despike]
[-p {27P,36P,24P,acompcor,aroma,acompcor_gsr,aroma_gsr,custom,none,gsr_only}]
[-c CUSTOM_CONFOUNDS] [--smoothing SMOOTHING] [-m]
[--motion-filter-type {lp,notch}] [--band-stop-min BPM]
[--band-stop-max BPM] [--motion-filter-order MOTION_FILTER_ORDER]
[-r HEAD_RADIUS] [-f FD_THRESH] [--min_time MIN_TIME]
[--disable-bandpass-filter] [--lower-bpf LOWER_BPF]
[--upper-bpf UPPER_BPF] [--bpf-order BPF_ORDER]
[--atlases {4S1056Parcels,4S156Parcels,4S256Parcels,4S356Parcels,4S456Parcels,4S556Parcels,4S656Parcels,4S756Parcels,4S856Parcels,4S956Parcels,Glasser,Gordon,HCP,Tian} [{4S1056Parcels,4S156Parcels,4S256Parcels,4S356Parcels,4S456Parcels,4S556Parcels,4S656Parcels,4S756Parcels,4S856Parcels,4S956Parcels,Glasser,Gordon,HCP,Tian} ...]
| --skip-parcellation] [--min_coverage MIN_COVERAGE]
[--exact-time EXACT_TIME [EXACT_TIME ...]]
[--random-seed _RANDOM_SEED] [-w WORK_DIR] [--clean-workdir]
[--resource-monitor] [--stop-on-first-crash] [--notrack]
[--fs-license-file FILE] [--warp-surfaces-native2std]
[--skip-dcan-qc]
fmri_dir output_dir {participant}
xcp_d: error: unrecognized arguments:
/var/spool/slurmd/job22059564/slurm_script: line 38: --cifti: command not found
Screenshots / relevant information:
While the --cifti and -s flags do not appear in the usage details of the output log, they do show up when invoked by the --help command.
Any help would be greatly appreciated!
Many thanks,
Roey