Trait Error when running confound correction

[RLYounk]

Hi, I'm running into the trait error:

TraitError(
traits.trait_errors.TraitError: The 'mask' trait of a MaskEPIInputSpec instance must be a pathlike object or string representing an existing file, but a value of '/template/Fischer344_template_mask.nii' <class 'str'> was specified.

when running confound correction. I ran the preprocessing step with the following code where the template was defined and had no issues:
docker run -it --rm -v /mnt/data/data/younk017/Fischer344_rat_atlas/Fischer344_nii_v4/:/template/ -v $PWD/bids_brkraw_orient:/bids_brkraw_orient:ro -v $PWD/OCF4_preprocess_outputs:/OCF4_preprocess_outputs ghcr.io/cobralab/rabies:latest -p MultiProc preprocess /bids_brkraw_orient/ /OCF4_preprocess_outputs/ --isotropic_HMC --detect_dummy --anat_robust_inho_cor apply=true,masking=false,brain_extraction=false,template_registration=SyN --bold_robust_inho_cor apply=true,masking=false,brain_extraction=false,template_registration=SyN --apply_STC --TR 1 --tpattern alt-z --labels /template/Fischer344_tissueClassification.nii.gz --WM_mask /template/Fischer344_TPM_WM_bin.nii.gz --CSF_mask /template/Fischer344_TPM_CSF_bin.nii.gz --brain_mask /template/Fischer344_template_mask.nii --anat_template /template/Fischer344_template.nii --vascular_mask /template/Fischer344_TPM_other_bin.nii.gz

The error is coming up when running this confound correction:
docker run -it --rm -v $PWD/bids_brkraw_orient:/bids_brkraw_orient:ro -v $PWD/OCF4_preprocess_outputs:/OCF4_preprocess_outputs/ -v $PWD/OCF4_confound_correction_outputs:/OCF4_confound_correction_outputs ghcr.io/cobralab/rabies:latest -p MultiProc confound_correction /OCF4_preprocess_outputs/ /OCF4_confound_correction_outputs/ --conf_list WM_signal CSF_signal mot_24 aCompCor_percent --frame_censoring FD_censoring=true,FD_threshold=0.05,DVARS_censoring=false,minimum_timepoint=3 --TR 1 --generate_CR_null
This produces the following error with traceback:

Traceback (most recent call last):
File "/opt/conda/bin/rabies", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/home/mambauser/RABIES/scripts/rabies", line 3, in
execute_workflow()
File "/home/mambauser/RABIES/rabies/run_main.py", line 53, in execute_workflow
workflow = confound_correction(opts, log)
File "/home/mambauser/RABIES/rabies/run_main.py", line 269, in confound_correction
workflow = init_main_confound_correction_wf(preprocess_opts, opts)
File "/home/mambauser/RABIES/rabies/confound_correction_pkg/main_wf.py", line 24, in init_main_confound_correction_wf
split_dict, split_name, target_list = read_preproc_workflow(preproc_output, nativespace=cr_opts.nativespace_analysis)
File "/home/mambauser/RABIES/rabies/confound_correction_pkg/main_wf.py", line 310, in read_preproc_workflow
node_dict = get_workflow_dict(preproc_workflow_file)
File "/home/mambauser/RABIES/rabies/utils.py", line 488, in get_workflow_dict
graph = pickle.load(handle)
File "/opt/conda/lib/python3.9/site-packages/traits/has_traits.py", line 1399, in setstate
self.trait_set(trait_change_notify=trait_change_notify, **state)
File "/opt/conda/lib/python3.9/site-packages/traits/has_traits.py", line 1509, in trait_set
setattr(self, name, value)
File "/opt/conda/lib/python3.9/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/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/opt/conda/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'mask' trait of a MaskEPIInputSpec instance must be a pathlike object or string representing an existing file, but a value of '/template/Fischer344_template_mask.nii' <class 'str'> was specified.

Can you help with this? Thank you!

[RLYounk]

I ended up solving this issue. I needed to add the local atlas to the template again in confound correction
The confound correction input that worked:
docker run -it --rm -v /mnt/data/data/younk017/Fischer344_rat_atlas/Fischer344_nii_v4/:/template/ -v $PWD/bids_brkraw_orient:/bids_brkraw_orient:ro -v $PWD/OCF4_preprocess_outputs:/OCF4_preprocess_outputs/ -v $PWD/OCF4_confound_correction_outputs:/OCF4_confound_correction_outputs ghcr.io/cobralab/rabies:latest -p MultiProc confound_correction /OCF4_preprocess_outputs/ /OCF4_confound_correction_outputs/ --conf_list WM_signal CSF_signal mot_24 aCompCor_percent --frame_censoring FD_censoring=true,FD_threshold=0.05,DVARS_censoring=false,minimum_timepoint=3 --TR 1 --generate_CR_null