Summary of what happened:
Hi, sorry if this is a silly question, but I’m having trouble choosing one of the 4S atlas resolutions. Am I not using the correct syntax? Code below.
Command used:
#!/bin/bash
#$ -N sub-SUBJECT_xcp_d
#$ -pe smp 25
OMP_NUM_THREADS=10
singularity run --cleanenv -H ${HOME}/singularity_home -B /Shared/MRRCdata/Bipolar_MDD:/mnt \
/Shared/MRRCdata/Programs/xcp-d/xcp_d-0.6.0.simg \
/mnt/derivatives/fmriprep/v23-1-2 \
/mnt/derivatives/xcp-d/v0-6-0 \
participant --participant_label SUBJECT \
--dummy-scans 10 \
-f 0.5 \
--atlases 4S456Parcels
Version:
0.6.0
Environment:
Singularity / Apptainer
Error log output:
usage: xcp_d [-h] [--version]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[-t TASK_ID] [--bids-filter-file FILE] [-m] [-s]
[--nthreads NTHREADS] [--omp-nthreads OMP_NTHREADS]
[--mem_gb MEM_GB] [--use-plugin USE_PLUGIN] [-v]
[--input-type {fmriprep,dcan,hcp,nibabies}]
[--smoothing SMOOTHING] [--despike]
[-p {27P,36P,24P,acompcor,aroma,acompcor_gsr,aroma_gsr,custom,none}]
[-c CUSTOM_CONFOUNDS] [--min_coverage MIN_COVERAGE]
[--min_time MIN_TIME] [--dummy-scans {{auto,INT}}]
[--random-seed _RANDOM_SEED] [--disable-bandpass-filter]
[--lower-bpf LOWER_BPF] [--upper-bpf UPPER_BPF]
[--bpf-order BPF_ORDER] [--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] [--exact-time EXACT_TIME [EXACT_TIME ...]]
[-w WORK_DIR] [--clean-workdir] [--resource-monitor] [--notrack]
[--fs-license-file FILE] [--warp-surfaces-native2std] [--dcan-qc]
fmri_dir output_dir {participant}
xcp_d: error: unrecognized arguments: --atlases 4S456Parcels
Thank you