Summary of what happened:
Hello,
Sincere apologies if this has been resolved before. I tried to go through the topics to find this and see that this error has occur before but I cannot figure out why I am getting it.
I get the following crash report. Can you tell my why I get this error and how I could fix it?
thank you!
Command used (and if a helper script was used, a link to the helper script or the command generated):
PASTE CODE HERE
Version:
PUT VERSION HERE
Environment (Docker, Singularity / Apptainer, custom installation):
I am running python 3.11 and fmriprep_docker on a Mac M3 Pro
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Node: _denoise1
Working directory: /tmp/work/fmriprep_24_1_wf/sub_9001_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise1
Node inputs:
args = <undefined>
dimension = <undefined>
environ = {'NSLOTS': '8'}
input_image = /data/sub-9001/ses-2/anat/sub-9001_ses-2_T1w.nii.gz
noise_image = <undefined>
noise_model = Rician
num_threads = 8
output_image = <undefined>
save_noise = False
shrink_factor = 1
verbose = <undefined>
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 _denoise1.
Cmdline:
DenoiseImage -i /data/sub-9001/ses-2/anat/sub-9001_ses-2_T1w.nii.gz -n Rician -o sub-9001_ses-2_T1w_noise_corrected.nii.gz -s 1
Stdout:
Stderr:
Killed
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/opt/conda/envs/fmriprep/lib/python3.11/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/python3.11/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'output_image' trait of a DenoiseImageOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/fmriprep_24_1_wf/sub_9001_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise1/sub-9001_ses-2_T1w_noise_corrected.nii.gz' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 400, in run
outputs = self.aggregate_outputs(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/fmriprep_24_1_wf/sub_9001_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise1/sub-9001_ses-2_T1w_noise_corrected.nii.gz' for output 'output_image' of a DenoiseImage interface