Summary of what happened:
I’m using fMRIPrep 24.1.0 on a subset (N=40) of the Narratives dataset, there are two subjects failed due to the same reason:
Extreme value 2.21e+04 detected in spline coefficients
when running "fmriprep_24_1_wf.sub_095_wf.fmap_preproc_wf.wf_auto_00004.bs_filter"
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv \
-B /om2/scratch/tmp/yibei/fmriprep_compute/job-38898175-sub-095/ds \
-B /nese/mit/group/sig/projects/hbn/hbn_bids/code/license.txt:/SGLR/FREESURFER_HOME/license.txt \
containers/.datalad/environments/fmriprep-24-1-0/image \
inputs/data/BIDS \
outputs/fmriprep \
participant \
-w /om2/scratch/tmp/yibei/fmriprep_compute/job-38898175-sub-095/ds/.git/tmp/wkdir
--nthreads 16 \
--omp-nthreads 8 \
--mem-mb 40000 \
--low-mem --stop-on-first-crash \
--fs-license-file /SGLR/FREESURFER_HOME/license.txt \
--skip-bids-validation \
--force-bbr \
--fd-spike-threshold 0.9 \
--dvars-spike-threshold 5 \
--cifti-output 91k \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym \
--use-syn-sdc \
--notrack \
--medial-surface-nan \
-v -v \
--participant-label sub-095
Version: fMRIPrep 24.1.0
Environment (Docker, Singularity / Apptainer, custom installation): Singularity (within BABS)
Data formatted according to a validatable standard? Please provide the output of the validator: BIDS
Relevant log outputs (up to 20 lines):
Working directory: /om2/scratch/tmp/yibei/fmriprep_compute/job-38898175-sub-095/ds/.git/tmp/wkdir/fmriprep_24_1_wf/sub_095_wf/fmap_preproc_wf/wf_auto_00004/bs_filter
Node inputs:
bs_spacing = [(100.0, 100.0, 40.0), (16.0, 16.0, 10.0)]
debug = False
extrapolate = True
in_data = <undefined>
in_mask = <undefined>
recenter = False
ridge_alpha = 0.0001
zooms_min = 1.0
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node bs_filter.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/sdcflows/interfaces/bspline.py", line 225, in _run_interface
raise RuntimeError(
RuntimeError: Spline fit of input file /om2/scratch/tmp/yibei/fmriprep_compute/job-38898175-sub-095/ds/.git/tmp/wkdir/fmriprep_24_1_wf/sub_095_wf/fmap_preproc_wf/wf_auto_00004/zooms_field/fmap_syn0Warp_Hz_trans.nii.gz failed. Extreme value 2.21e+04 detected in spline coefficients.