So when I run it I get:
(base) me@mes-MacBook-Air ~ % ls ml_projects/fMRIprep/raw/output
dataset_description.json desc-aseg_dseg.tsv sourcedata sub-01.html
desc-aparcaseg_dseg.tsv logs sub-01
The folder “raw” is where the raw data is which was also BIDs formatted. The output of fMRIprep is the “output” folder (so the raw and fmriprep preprocessed data aren’t separated). Maybe it’s the “sub-01” folder which is what contains the anat and func preprocessed data that I need to send to xcp? “sub-01” contains:
(base) me@mes-MacBook-Air ~ % ls ml_projects/fMRIprep/raw/output/sub-01
anat figures func log
I was also trying to run a stripped down version of the command in order to debug it one line at a time and I’m finding that it is also not finding the freesurfer license.txt which is weird as it is at the specified location:
(base) me@mes-MacBook-Air ~ % docker run --rm -it -v ~/ml_projects/fmriprep/freesurfer:/freesurfer:ro pennlinc/xcp_d:latest . /out participant --fs-license-file license.txt
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
usage: xcp_d [-h] [--version] [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-t TASK_ID] [--bids-filter-file FILE]
[--bids-database-dir PATH] [-s] [--nprocs NPROCS] [--omp-nthreads OMP_NTHREADS] [--mem-gb MEMORY_GB] [--low-mem]
[--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 HIGH_PASS] [--upper-bpf LOW_PASS] [--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 ...]]
[--aggregate-session-reports AGGR_SES_REPORTS] [--random-seed _RANDOM_SEED] [-w WORK_DIR] [--clean-workdir]
[--resource-monitor] [--config-file FILE] [--write-graph] [--stop-on-first-crash] [--notrack]
[--debug {pdb,all} [{pdb,all} ...]] [--fs-license-file FILE] [--md-only-boilerplate] [--boilerplate-only] [--reports-only]
[--warp-surfaces-native2std] [--skip-dcan-qc]
fmri_dir output_dir {participant}
xcp_d: error: Path does not exist: <license.txt>.
Thanks in advance for your help!