Hi Dr. Arfanakis,

I encountered the following error while running ARTS:

Chris Rorden's dcm2niiX version v1.0.20211006  GCC5.4.0 x86-64 (64-bit Linux)
Found 208 DICOM file(s)
Warning: Assuming mosaics saved in reverse order due to 'sSliceArray.ucImageNumb'
Convert 208 DICOM as /output/T1/input_T1_Accelerated_Sagittal_MPRAGE_(MSV21)_20230331141122_2 (240x256x208x1)
Conversion required 0.197847 seconds (0.196674 for core code).
sh: 1: Syntax error: "(" unexpected
Traceback (most recent call last):
  File "/opt/miniconda-latest/envs/main/lib/python3.7/site-packages/nibabel/loadsave.py", line 42, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/output/T1/T1.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/biokit/scripts/preprocessing/run_preprocessing.py", line 27, in <module>
    preprocess.run()
  File "/opt/biokit/scripts/preprocessing/Preprocess.py", line 49, in run
    self.__prepare_structural_data(path_to_data=self.path_t1, type_of_data=self.datatype_t1, mri_datatype='T1')
  File "/opt/biokit/scripts/preprocessing/Preprocess.py", line 193, in __prepare_structural_data
    if self.__has_multiple_echoes(nifti_file=nifti_path):
  File "/opt/biokit/scripts/preprocessing/Preprocess.py", line 223, in __has_multiple_echoes
    img = nib.load(nifti_file)
  File "/opt/miniconda-latest/envs/main/lib/python3.7/site-packages/nibabel/loadsave.py", line 44, in load
    raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/output/T1/T1.nii.gz'

From looking at this output, I think the parantheses in the series description are causing the issue. If you could please patch ARTS to not use the series description when making the NIfTI file using dcm2niix, that would be great. 

Thanks,

Mike

Hello Mike,

I am the developer of ARTS. Thank you for reporting this bug. I was able to reproduce the error using a dataset with parenthesis in the SeriesDescription. This bug is fixed in the new version of ARTS (v1.1.1) that will be uploaded early next week. Let us know if you have any other issues with the new version.

Best,

Arnold 

Great! Thanks, Arnold.

Mike

Hi Mike,

The new version is now available. You should not have any problems with parentheses any more. Please let us know if you have any other questions.

Konstantinos