Summary of what happened:
Hi, I am running fmriprep on mouse data - I have added the DSURQE mouse template to my templateflow directory, but fmriprep still also uses the default human template.
In the command, I specify output_spaces to use ‘DSURQE:res-3’ which I have verified exists and looks as expected. fmriprep in fact did create relevant folders such as fmriprep_23_1_wf/single_subject_LD23_wf/func_preproc_ses_chronic_task_resting_wf/bold_std_trans_wf/_std_target_DSURQE.res3 and populated them so I do believe fmriprep has seen and attempted using the atlas I want. However, it still tries to perform registration to the default _std_target_MNI152NLin2009cAsym. atlas as seen from my error message below. This folder does indeed exist in the output folder as well. In the DSURQE output folder, the missing file fmriprep is complaining about (vol0000_xform-00000_clipped_merged_sliced_md.1D) is missing too.
Am I doing something wrong such that the gen_avg.a1 process cannot run? Or is it to do with the default template being unsuitable for my mouse data? If so, how force fmriprep to only use the DSURQE atlas?
Thank you.
Command run:
fmriprep /home/tanjazl1/scratch/fmriprep_test \
/home/tanjazl1/scratch/fmriprep_test_output \
participant \
--verbose --skip-bids-validation \
-w /home/tanjazl1/scratch/fmriprep_test_output \
--fs-license-file /home/tanjazl1/scratch/fmriprep_test_output/freesurfer_liscence.txt \
--output-spaces DSURQE:res-3 \
--anat-derivatives /home/tanjazl1/scratch/fmriprep_test_output/anat_derivatives \
--fs-no-reconall --skull-strip-template DSURQE:res-3 \
--ignore fieldmaps
Templateflow directory
scratch/templateflow/tpl-DSURQE/
├── template_description.json
├── tpl-DSURQE_res-1_desc-brain_mask.nii.gz
├── tpl-DSURQE_res-1_dseg.nii.gz
├── tpl-DSURQE_res-1_T1w.nii.gz
├── tpl-DSURQE_res-2_desc-brain_mask.nii.gz
├── tpl-DSURQE_res-2_dseg.nii.gz
├── tpl-DSURQE_res-2_T1w.nii.gz
├── tpl-DSURQE_res-3_desc-brain_mask.nii.gz
├── tpl-DSURQE_res-3_dseg.nii.gz
└── tpl-DSURQE_res-3_T1w.nii.gz
Error message:
250226-01:45:36,960 nipype.workflow ERROR:
could not run node: fmriprep_23_1_wf.single_subject_LD23_wf.func_preproc_ses_chronic_task_resting_wf.bold_std_trans_wf.bold_reference_wf.gen_avg.a1
250226-01:45:36,964 nipype.workflow INFO:
crashfile: /home/tanjazl1/scratch/fmriprep_test_output/sub-LD23/log/20250225-225529_b3a2b34a-b923-481f-9314-6e78ec980880/crash-20250226-010254-tanjazl1-gen_avg.a1-2f65bc7b-1de5-4d77-ad29-01e8cf94fa7f.txt
250226-01:45:36,964 nipype.workflow INFO:
***********************************
250226-01:45:37,315 nipype.workflow CRITICAL:
fMRIPrep failed: 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 gen_avg.
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 'md1d_file' trait of a VolregOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/home/tanjazl1/scratch/fmriprep_test_output/fmriprep_23_1_wf/single_subject_LD23_wf/func_preproc_ses_chronic_task_resting_wf/bold_std_trans_wf/bold_reference_wf/_std_target_MNI152NLin2009cAsym./gen_avg/vol0000_xform-00000_clipped_merged_sliced_md.1D' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/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/images.py", line 337, in _run_interface
res = volreg.run()
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 '/home/tanjazl1/scratch/fmriprep_test_output/fmriprep_23_1_wf/single_subject_LD23_wf/func_preproc_ses_chronic_task_resting_wf/bold_std_trans_wf/bold_reference_wf/_std_target_MNI152NLin2009cAsym./gen_avg/vol0000_xform-00000_clipped_merged_sliced_md.1D' for output 'md1d_file' of a Volreg interface
Version and environment:
I am using Compute Canada’s fmriprep version 23.1.3. My data is in BIDS structure although there is only a single subject and session for now while I am testing fmriprep.