Summary of what happened:
I am preprocessing my data with fMRIPrep. Upon review of the subject-wise .html files, it seems that there is a common error throughout: Node Name: fmriprep_23_2_wf.sub_SL001_wf.anat_fit_wf.register_template_wf.registration
Despite this error, the pipeline runs to completion as there is a .../func/*desc-preproc_bold.* for each participant, indicating a fully preprocessed subject.
Any help in ensuring that my data is properly processed would be great.
Command used (and if a helper script was used, a link to the helper script or the command generated):
The script used to run fMRIPrep is located on my Github, here. This script contains the individual commands.
Below is the command to execute the aforementioned script.
sh run_fmriprep_singularity.sh -b /path/to/bids/dir -w /path/to/work/dir
The basic fmriprep command is:
singularity run --cleanenv -B /data/jdecke5:/data/jdecke5 $HOME/images/fmriprep.simg \
--work-dir $work_dir_parent/workdir \
--participant_label "${sub##*/sub-}" \
--output-spaces T1w \
--level full \
--skip-bids-validation \
--fs-license-file $FREESURFER_HOME/license.txt \
--cifti-output 91k \
$bids_dir \
$bids_dir/derivatives \
participant
Version:
v23.1.2
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Relevant log outputs
# File: /data/jdecke5/projects/honors-thesis/data/bids/derivatives/sub-SL001/log/20240318-105148_2ce66d62-8223-46c7-aeaa-9116724367ac/crash-20240318-111519-jdecke5-registration.a1-dc527342-2b1d-4909-bab3-e2e5571bb651.txt
Working Directory: /data/jdecke5/projects/honors-thesis/data/raw/workdir/workdir/fmriprep_23_2_wf/sub_SL001_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin6Asym/registration
Inputs:
explicit_masking: True
flavor: precise
float: True
initial_moving_transform:
lesion_mask:
moving: T1w
moving_image:
moving_mask:
num_threads: 8
orientation: RAS
reference: T1w
reference_image:
reference_mask:
settings:
template: MNI152NLin2009cAsym
template_resolution:
template_spec:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/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 registration.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/norm.py", line 182, in _run_interface
ants_args = self._get_ants_args()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/norm.py", line 457, in _get_ants_args
args["fixed_image"] = mask(
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/norm.py", line 506, in mask
data = in_nii.get_fdata()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/dataobj_images.py", line 373, in get_fdata
data = np.asanyarray(self._dataobj, dtype=dtype)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/arrayproxy.py", line 439, in __array__
arr = self._get_scaled(dtype=dtype, slicer=())
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/arrayproxy.py", line 406, in _get_scaled
scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/arrayproxy.py", line 376, in _get_unscaled
return array_from_file(
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/volumeutils.py", line 472, in array_from_file
raise OSError(
OSError: Expected 14442064 bytes, got 1043566 bytes from object
- could the file be damaged?Relevant log outputs (up to 20 lines):