Summary of what happened:
I am pre-processing anatomical (T1) and functional data for multiple subjects. While I have successfully pre-processed 21 subjects, the last 7 return an error that I believe is resulting in a lack of confound_timeseries.tsv file, which is needed for the next step in our analysis. All subjects input data is in BIDS format, all of which is the same, so it is unclear why this error is now occurring. The error relates to: Node Name: fmriprep_23_2_wf.sub_WLfMRI041_wf.anat_fit_wf.fast
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep-docker /Users/lendlab/Desktop/WL_fMRI/data/BIDS /Users/lendlab/Desktop/WL_fMRI/data/derivatives/fmriprep participant --participant-label sub-WLfMRI033 --fs-license-file /Users/lendlab/Desktop/WL_fMRI/license.txt --bids-filter-file /Users/lendlab/Desktop/WL_fMRI/anat_filter_JMS.py
Version:
23.2.3
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
I do not have the output to provide, however, no errors are reported (there are some warnings). The BIDS data that has run successfully is formatted the same as the BIDS data that is not running successfully.
Relevant log outputs (up to 20 lines):
Node Name: fmriprep_23_2_wf.sub_WLfMRI041_wf.anat_fit_wf.fast
File: /out/sub-WLfMRI041/log/20240925-202014_d1b38fee-cd4b-444d-8cb3-2ec372f74399/crash-20240926-013018-root-fast-ec8b9450-7279-4f9e-869c-5c15b8b24210.txt
Working Directory: /tmp/work/fmriprep_23_2_wf/sub_WLfMRI041_wf/anat_fit_wf/fast
Inputs:
args:
bias_iters:
bias_lowpass:
environ: {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
hyper:
img_type:
in_files:
init_seg_smooth:
init_transform:
iters_afterbias:
manual_seg:
mixel_smooth:
no_bias: True
no_pve:
number_classes:
other_priors:
out_basename:
output_biascorrected:
output_biasfield:
output_type: NIFTI_GZ
probability_maps: True
segment_iters:
segments: True
use_priors:
verbose:
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 fast.
Cmdline:
fast -N -p -g -S 1 /tmp/work/fmriprep_23_2_wf/sub_WLfMRI041_wf/anat_fit_wf/fast/sub-WLfMRI041_ses-Session2_T1w_noise_corrected_corrected_xform_masked.nii.gz
Stdout:
Stderr:
Killed
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'tissue_class_map' trait of a FASTOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/fmriprep_23_2_wf/sub_WLfMRI041_wf/anat_fit_wf/fast/sub-WLfMRI041_ses-Session2_T1w_noise_corrected_corrected_xform_masked_seg.nii.gz' was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
outputs = self.aggregate_outputs(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/fmriprep_23_2_wf/sub_WLfMRI041_wf/anat_fit_wf/fast/sub-WLfMRI041_ses-Session2_T1w_noise_corrected_corrected_xform_masked_seg.nii.gz' for output 'tissue_class_map' of a FAST interface```
### Screenshots / relevant information:
Processing system:
macOS Catalina
Version 10.15.7
Processor: 3.4 GHz Quad-Core Intel Core i7
Memory: 8 GB 1600 MHz DDR3
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