Preprocessing Failed

[agryshyna]

Hello!

I am trying to figure out why my preprocessing step is failing when I try to run my mouse fmri scans that were collected on Burker 9.4T imager. It looks like some of the files could not be opened but I checked all of the permissions to make sure that there is a writing and execution permission for all users. Specifically, the first error indicates that modelfile.mnc could not be opened but it does exist in the directory and has the permissions for execution. My script is displayed below with some of the errors that I got (there
rabies_complete_script.txt
are a lot more errors in the script). Thank you for your help in advance!

$rabies -p MultiProc preprocess input_BIDS/ preprocess_outputs/ --apply_STC --TR 1.42 --commonspace_reg masking=false,brain_extraction=false,template_registration=SyN,fast_commonspace=false
```

Errors:
```
/mnt/c/Users/Anastasiia/build/ITKv5/Modules/ThirdParty/MINC/src/libminc/libsrc2/volume.c:1403 (from MINC): Unable to open file '/tmp/tmp.G5sd8YNNFp/modelfile.mnc'
Exception caught during reference file reading

itk::ExceptionObject (0x55af63e046d0)
Location: "unknown"
File: /mnt/c/Users/Anastasiia/build/ITKv5/Modules/IO/MINC/src/itkMINCImageIO.cxx
Line: 312
Description: ITK ERROR: MINCImageIO(0x55af63dfd6e0): Could not open file "/tmp/tmp.G5sd8YNNFp/modelfile.mnc".

Traceback:
        Traceback (most recent call last):
          File "/home/agryshyna/.local/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
            runtime = self._run_interface(runtime)
          File "/home/agryshyna/.local/lib/python3.10/site-packages/rabies/preprocess_pkg/inho_correction.py", line 280, in _run_interface
            rc = run_command(command)
          File "/home/agryshyna/.local/lib/python3.10/site-packages/rabies/utils.py", line 354, in run_command
            process = subprocess.run(
          File "/usr/lib/python3.10/subprocess.py", line 526, in run
            raise CalledProcessError(retcode, process.args,
        subprocess.CalledProcessError: Command 'structural-preprocessing.sh /mnt/c/Users/Anastasiia/Desktop/dataset_fmri/preprocess_outputs/main_wf/anat_inho_cor_wf/_scan_info_subject_id7360.session1_split_name_sub-7360_ses-1_acq-RARE_T2w/InhoCorrection/sub-7360_ses-1_acq-RARE_T2w_RAS_resampled.nii.gz /mnt/c/Users/Anastasiia/Desktop/dataset_fmri/preprocess_outputs/main_wf/anat_inho_cor_wf/_scan_info_subject_id7360.session1_split_name_sub-7360_ses-1_acq-RARE_T2w/InhoCorrection/sub-7360_ses-1_acq-RARE_T2w_RAS_inho_cor.nii.gz /mnt/c/Users/Anastasiia/Desktop/dataset_fmri/preprocess_outputs/main_wf/resample_template/resampled_template.nii.gz /mnt/c/Users/Anastasiia/Desktop/dataset_fmri/preprocess_outputs/main_wf/resample_template/resampled_mask.nii.gz SyN false 2' returned non-zero exit status 134.
```

[Gab-D-G]

Hi, I can see you are using a local installation of RABIES. This looks like a dependency error arising from your installation of minc-toolkit or ANTs. Any reason why you are not using Singularity or Docker?