Summary of what happened:
Dear experts,
I’ve recently started to learn fMRIPrep to preprocess our resting-state fMRI data. I tried the pipeline according to the descriptions in Docs, but I noticed that if I added the --cifti-output flag, I get an error about conf_plot. However, the carpetplot appears to be generated successfully. On the other hand, the grayordinate files are not generated in the out/func directory.
I’ve confirmed that the above error does not occur and fMRIPrep finishes successfully if I don’t use the --cifti-output flag.
Command used (and if a helper script was used, a link to the helper script or the command generated):
Here is the command I used.
fmriprep-docker $bids_root_dir $bids_root_dir/derivatives \
participant \
-w $HOME \
--skip-bids-validation \
--participant-label $subj \
--nthreads $nthreads \
--mem-mb $mem_mb \
--low-mem \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-native \
--md-only-boilerplate \
--output-layout bids \
--medial-surface-nan \
--bold2t1w-init register \
--bold2t1w-dof 6 \
--force-bbr \
--random-seed 0 \
--project-goodvoxels \
--cifti-output \
--use-aroma \
--error-on-aroma-warnings \
--return-all-components \
--fd-spike-threshold 0.5 \
--dvars-spike-threshold 1.5 \
--skull-strip-template OASIS30ANTs \
--skull-strip-fixed-seed \
--skull-strip-t1w force \
--fs-license-file $FS_LICENSE \
--write-graph \
--stop-on-first-crash
Version:
23.0.1
Environment (Docker, Singularity, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
I confirmed that my data structure is in line with BIDS standards, using the BIDS validator.
Relevant log outputs (up to 20 lines):
The error log is below. Although " Finished “gen_cifti” " is displayed, grayordinates files are not generated in out/func.
230502-00:18:42,631 nipype.workflow INFO:
[Node] Executing "gen_cifti" <niworkflows.interfaces.cifti.GenerateCifti>
230502-00:19:06,630 nipype.workflow INFO:
[Node] Finished "gen_cifti", elapsed time 23.997285s.
230502-00:19:08,630 nipype.workflow INFO:
[Node] Setting-up "fmriprep_23_0_wf.single_subject_N0001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot" in "/scratch/fmriprep_23_0_wf/single_subject_N0001_wf/func_preproc_task_rest_wf/carpetplot_wf/conf_plot".
230502-00:19:08,631 nipype.workflow INFO:
[Node] Outdated cache found for "fmriprep_23_0_wf.single_subject_N0001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot".
230502-00:19:08,676 nipype.workflow INFO:
[Node] Executing "conf_plot" <fmriprep.interfaces.confounds.FMRISummary>
230502-00:19:11,751 nipype.workflow INFO:
[Node] Finished "conf_plot", elapsed time 3.062313s.
230502-00:19:11,751 nipype.workflow WARNING:
Storing result file without outputs
230502-00:19:11,756 nipype.workflow WARNING:
[Node] Error on "fmriprep_23_0_wf.single_subject_N0001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot" (/scratch/fmriprep_23_0_wf/single_subject_N0001_wf/func_preproc_task_rest_wf/carpetplot_wf/conf_plot)
230502-00:19:12,697 nipype.workflow ERROR:
Node conf_plot failed to run on host 3c643796fd03.
230502-00:19:12,704 nipype.workflow ERROR:
Saving crash info to /out/sub-N0001/log/20230501-102240_cf4fc7fe-1369-4d9c-a842-9eeb89ecc41e/crash-20230502-001912-root-conf_plot-ad732c91-f9f6-4199-aae7-13a664cc02d7.txt
Screenshots / relevant information:
Another concern is that no “sub-<subject_label>_[specifiers]_space-<space_label>_hemi-[LR]_bold.func.gii” files are generated in my out/func directory. What does this have to do with the above error?
I would be grateful for the knowledge of possible causes and solutions. Please point out any missing information.
Sincerely yours,