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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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fMRIPrep preprocessing problem #3318

Open Chen1997237 opened 1 month ago

Chen1997237 commented 1 month ago

What happened?

Hi, I'm very new to fmriprep. I followed a tutorial to have it installed with docker and then after running in my BIDS data, but I got errors, even if I have tried many times. Thank you!

What command did you use?

fmriprep-docker ./Nifiti ./Nifiti/derivatives participant --dummy-scans 1 --fs-no-reconall --fs-license-file ./license.txt -w .
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=26.1.4 -it -v /mnt/e/VerbalFluenc/license.txt:/opt/freesurfer/license.txt:ro -v /mnt/e/VerbalFluenc/Nifiti:/data:ro -v /mnt/e/VerbalFluenc/Nifiti/derivatives:/out -v /mnt/e/VerbalFluenc:/scratch nipreps/fmriprep:24.0.0 /data /out participant --dummy-scans 1 --fs-no-reconall -w /scratch

What version of fMRIPrep are you running?

24.0.0

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

[Node] Finished "conf_plot", elapsed time 2.935544s.
240705-08:24:24,889 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_04_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,908 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_01_wf.anat_fit_wf.fast
240705-08:24:24,921 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_05_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,925 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_06_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,929 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_08_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,933 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_07_wf.anat_fit_wf.fast
240705-08:24:24,937 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_02_wf.anat_fit_wf.fast
240705-08:24:24,941 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_10_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,945 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_03_wf.anat_fit_wf.fast
240705-08:24:24,950 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_12_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,954 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_11_wf.anat_fit_wf.fast
240705-08:24:24,958 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_14_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,962 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_09_wf.anat_fit_wf.fast
240705-08:24:24,966 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_15_wf.anat_fit_wf.fast
240705-08:24:24,970 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_18_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,974 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_13_wf.anat_fit_wf.fast
240705-08:24:24,978 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_20_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,982 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_21_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:24,986 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_16_wf.anat_fit_wf.fast
240705-08:24:24,991 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_19_wf.anat_fit_wf.fast
240705-08:24:24,995 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_23_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
         could not run node: fmriprep_24_0_wf.sub_17_wf.anat_fit_wf.fast
240705-08:24:25,3 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_26_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.inu_n4_final
240705-08:24:25,7 nipype.workflow ERROR:
         could not run node: fmriprep_24_0_wf.sub_22_wf.anat_fit_wf.fast
240705-08:24:26,724 nipype.workflow CRITICAL:
         fMRIPrep failed: 24 raised. Re-raising first.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues

Additional information / screenshots

No response

effigies commented 1 month ago

Unfortunately, there are no errors shown here. Can you provide the full logs?