Summary of what happened:
I am trying to run the Xcp_d for resting state fMRI data, which was preprocessed using fMRIprep and the output of fMRIprep were in nifti format. When I run the Xcp_d, it throwing me the error:
xcp_d: error: unrecognized arguments: --file-format nifti
xcp-0.6.0_code.sh: line 34: [: : integer expression expected
Please help me to solve this issue. Below I pest the command I ran…
Command used (and if a helper script was used, a link to the helper script or the command generated):
# Set up the directories
fmriprep_dir="/data/RP/nifti/derivatives/fmriprep-23.1.4/sub-RP01/"
output_dir="/data/RP/nifti/derivatives/fmriprep-23.1.4/derivatives"
working_dir="/working/RP/sub-RP01"
fs_license="/home/Documents/freesurfer_license_sr.txt"
confounds_file="${fmriprep_dir}/confounds/sub-RP01"
xcp_img="/data/software/xcp_d-0.6.0.simg"
singularity_command="singularity run --cleanenv \
${xcp_img} \
${fmriprep_dir} ${output_dir} participant \
--participant-label sub-RP01 \
-w ${working_dir} \
--fs-license-file ${fs_license} \
--input-type fmriprep \
--smoothing 6 \
--nuisance-regressors custom \
--custom-confounds ${confounds_file} \
--dummy-scans 6 \
--lower-bpf 0.008 \
--upper-bpf 0.1 \
--motion-filter-type notch \
--band-stop-min 12 \
--band-stop-max 18 \
--head-radius auto \
--fd-thresh 0 \
--file-format nifti"
Version:
xcp_d-0.6.0
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
fMRIprep
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
xcp_d: error: unrecognized arguments: --file-format nifti
xcp-0.6.0_code.sh: line 34: [: : integer expression expected