When running fmriprep on a new subject, slice timing correction has failed for only one of its 10 bold runs (extinction). This particular error has only occurred for this one subject. Would appreciate any help or guidance, the slice_timing in the json for this subject’s extinction run is the same as all the other subjects’ extinction jsons. Here is the crash report:
Node: fmriprep_wf.single_subject_CCX010_wf.func_preproc_ses_1_task_extinction_wf.bold_stc_wf.slice_timing_correction
Working directory: /scratch/06866/nkell12/fmriprep/fmriprep_wf/single_subject_CCX010_wf/func_preproc_ses_1_task_extinction_wf/bold_stc_wf/slice_timing_correction
Node inputs:
args =
environ = {}
ignore = 1
in_file = /scratch/06866/nkell12/CCX-bids-current/sub-CCX010/ses-1/func/sub-CCX010_ses-1_task-extinction_bold.nii.gz
interp =
num_threads = 1
out_file =
outputtype = NIFTI_GZ
rlt =
rltplus =
slice_encoding_direction = k
slice_timing = [0.002735, 0.0, 0.0028125, 7.75e-05, 0.0028875, 0.0001525, 0.0029625, 0.0002275, 0.00304, 0.000305, 0.003115, 0.00038, 0.0031925, 0.0004575, 0.0032675, 0.0005325, 0.0033425, 0.0006075, 0.00342, 0.000685, 0.003495, 0.00076, 0.00357, 0.000835, 0.0036475, 0.0009125, 0.0037225, 0.0009875, 0.0038, 0.001065, 0.003875, 0.00114, 0.00395, 0.001215, 0.0040275, 0.0012925, 0.0041025, 0.0013675, 0.00418, 0.001445, 0.004255, 0.00152, 0.00433, 0.001595, 0.0044075, 0.0016725, 0.0044825, 0.0017475, 0.0045575, 0.001825, 0.004635, 0.0019, 0.00471, 0.001975, 0.0047875, 0.0020525, 0.0048625, 0.0021275, 0.0049375, 0.0022025, 0.005015, 0.00228, 0.00509, 0.002355, 0.0051675, 0.0024325, 0.0052425, 0.0025075, 0.0053175, 0.0025825, 0.005395, 0.00266]
tpattern =
tr = 1s
tslice =
tzero = 0.003
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 521, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 639, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 751, in _run_command
f"Exception raised while executing Node {self.name}.\n\n{result.runtime.traceback}"
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node slice_timing_correction.
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 454, in aggregate_outputs
setattr(outputs, key, val)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 135, in validate
self.error(objekt, name, str(value))
File “/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_handlers.py”, line 172, in error
value )
traits.trait_errors.TraitError: The ‘out_file’ trait of a TShiftOutputSpec instance must be a pathlike object or string representing an existing file, but a value of ‘/scratch/06866/nkell12/fmriprep/fmriprep_wf/single_subject_CCX010_wf/func_preproc_ses_1_task_extinction_wf/bold_stc_wf/slice_timing_correction/sub-CCX010_ses-1_task-extinction_bold_tshift.nii.gz’ <class ‘str’> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 401, in run
outputs = self.aggregate_outputs(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 461, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory ‘/scratch/06866/nkell12/fmriprep/fmriprep_wf/single_subject_CCX010_wf/func_preproc_ses_1_task_extinction_wf/bold_stc_wf/slice_timing_correction/sub-CCX010_ses-1_task-extinction_bold_tshift.nii.gz’ for output ‘out_file’ of a TShift interface