Summary of what happened:
I am running xcp-d on fMRIPrep outputs, but it is persistently failing during the CIFTI smoothing step. It seems to suggest a problem with the fsLR template surface, which I’m unsure how to resolve.
Command used (and if a helper script was used, a link to the helper script or the command generated):
apptainer run --cleanenv --containall \
-B /mnt:/mnt \
-B $TEMPLATEFLOW_HOME:$TEMPLATEFLOW_HOME \
--env TEMPLATEFLOW_HOME=$TEMPLATEFLOW_HOME \
$xcpd_img \
${fmriprep_dir} \
${out_dir} \
participant \
--mode linc \
--participant-label ${sub_id} \
--input-type fmriprep \
--omp-nthreads 4 \
--nprocs 1 \
--mem-gb 120 \
--low-mem \
--atlases \
4S156Parcels \
4S256Parcels \
4S356Parcels \
4S456Parcels \
4S556Parcels \
4S656Parcels \
4S756Parcels \
4S856Parcels \
4S956Parcels \
4S1056Parcels \
Glasser \
--work-dir ${work_dir} \
--file-format ${file_format} \
--fs-license-file $FSLIC \
--stop-on-first-crash \
-v
Version:
0.9.1
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer
Relevant log outputs (up to 20 lines):
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node cifti_smoothing.
Cmdline:
wb_command -cifti-smoothing /mnt/sauce/littlab/data/Human_Data/BIDS_2026/jobs/xcpd/work/ses-research3T/fieldmapless/xcp_d_0_9_wf/sub_RID0445_wf/postprocess_0_wf/denoise_bold_wf/regress_and_filter_bold/filtered_denoised.dtseries.nii 2.547965400864057 2.547965400864057 COLUMN smoothed_filtered_denoised.dtseries.nii -left-surface /mnt/sauce/littlab/data/Human_Data/BIDS_2026/software/templateflow/tpl-fsLR/tpl-fsLR_hemi-L_den-32k_sphere.surf.gii -right-surface /mnt/sauce/littlab/data/Human_Data/BIDS_2026/software/templateflow/tpl-fsLR/tpl-fsLR_hemi-R_den-32k_sphere.surf.gii
Stdout:
Stderr:
While running:
wb_command -cifti-smoothing /mnt/sauce/littlab/data/Human_Data/BIDS_2026/jobs/xcpd/work/ses-research3T/fieldmapless/xcp_d_0_9_wf/sub_RID0445_wf/postprocess_0_wf/denoise_bold_wf/regress_and_filter_bold/filtered_denoised.dtseries.nii 2.547965400864057 2.547965400864057 COLUMN smoothed_filtered_denoised.dtseries.nii -left-surface /mnt/sauce/littlab/data/Human_Data/BIDS_2026/software/templateflow/tpl-fsLR/tpl-fsLR_hemi-L_den-32k_sphere.surf.gii -right-surface /mnt/sauce/littlab/data/Human_Data/BIDS_2026/software/templateflow/tpl-fsLR/tpl-fsLR_hemi-R_den-32k_sphere.surf.gii
ERROR: left surface has the wrong number of vertices