Summary of what happened:
Hi, I’m having trouble preprocessing multi-echo data, collected with a restricted/limited FOV. The pipeline runs successfully only when I remove the fieldmaps from the raw dataset and include just a single echo image (e.g., echo-01).
If I keep all echoes (echo-01, echo-02, and echo-03) but remove the fieldmaps, fMRIPrep crashes at node DVARS with: “ValueError: Cannot apply_along_axis when any iteration dimensions are 0”.
When I include the fieldmaps, the workflow fails at node DVARS with: “ValueError: array must contain infs or NaNs” This occurs even for non-multiecho data (e.g.: acq-DresdenWFat).
I’m quite perplexed and would appreciate any advice in how to proceed.
Command used:
singularity run --cleanenv \
-B $bids_root_dir:/data \
"$FMRIPREP" \
/data/sourcedata/raw /data/derivatives \
participant \
--participant-label "$subj" \
--skip-bids-validation \
--level full \
--fs-license-file /data/code/license.txt \
--output-spaces MNI152NLin2009cAsym anat \
--omp-nthreads "$omthreads" \
--nthreads "$nthreads" \
--me-t2s-fit-method curvefit \
--work-dir /data/work \
--stop-on-first-crash \
-vv
Version:
25.2.3
Environment:
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
bids-validator-output2.txt (214.5 KB)
bids-validator-output.txt (221.9 KB)
Relevant log outputs:
Node: fmriprep_25_2_wf.sub_01_ses_01-03_wf.bold_ses_01_task_localizer_acq_ME3TR1100_echo_01_wf.bold_confounds_wf.dvars
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/numpy/lib/_shape_base_impl.py", line 383, in apply_along_axis
raise ValueError(
ValueError: Cannot apply_along_axis when any iteration dimensions are 0
Node: fmriprep_25_2_wf.sub_01_ses_01-03_wf.bold_ses_01_task_localizer_acq_DresdenWFat_wf.bold_confounds_wf.dvars
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/numpy/lib/_function_base_impl.py", line 646, in asarray_chkfinite
raise ValueError(
ValueError: array must not contain infs or NaNs
Screenshots / relevant information:
inf-nans_crash.txt (3.3 KB)
dim-0_crash.txt (2.3 KB)