Problem encountered when skipping N4

[lundq163]

Describe the bug
When setting --N4 to False when running the container, an intermediate file is not getting produced which appears to result in a downstream error.

Expected behavior
The error results from -reorient-enhanced.nii.gz intermediate in particular not being produced. In previous tests with the --N4 arg set as default, this error did not occur.

Screenshots
Error Log:

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1053
NiftiImageIO (0x557274a180f0): ./Template/template.hdr is Analyze file and it's deprecated 

WARNING: In /tmp/SimpleITK-build/ITK/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx, line 1053
NiftiImageIO (0x557274a180f0): ./Template/template.hdr is Analyze file and it's deprecated 

/utils/utils.py:209: UserWarning: Any labeled images will be returned as a boolean array. Did you mean to use a boolean array?
  filled_mask = remove_small_holes(mask, area_threshold=area_threshold)
Traceback (most recent call last):
  File "/BME-X.py", line 355, in <module>
    main()
  File "/BME-X.py", line 305, in main
    enhanced_img = sitk.ReadImage(enhanced_path)
  File "/usr/local/lib/python3.8/site-packages/SimpleITK/extra.py", line 384, in ReadImage
    return reader.Execute()
  File "/usr/local/lib/python3.8/site-packages/SimpleITK/SimpleITK.py", line 8502, in Execute
    return _SimpleITK.ImageFileReader_Execute(self)
RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:91:
sitk::ERROR: The file "/app/data/test/sub-106525/ses-V03/anat/sub-106525_ses-V03_run-2_T1w-reorient-enhanced.nii.gz" does not exist.

Output Log:

Found 1 files for subject 106525 and session V03
Subject ID: 106525
Session ID: V03
Processing file: /app/data/test/sub-106525/ses-V03/anat/sub-106525_ses-V03_run-2_T1w.nii.gz
Reorient to RAI direction
Skip N4
Downsample to 1.6*1.6*1.6
Histogram matching
Skull stripping
Upsample to original space
Save brainmask
age_unit: years
sessions_tsv_age: /app/data/test/sub-106525/sub-106525_sessions.tsv 6
age_in_month 6
file_path_for_BMEX /app/data/test/sub-106525/ses-V03/anat
Model:  ./BME_X/checkpoints/BMEX-Month6-T1-model.pt
Reference image: Template-Month6-T1w.nii.gz

Desktop (please complete the following information):

• OS: Linux
• Run Command: /usr/bin/singularity exec --pwd / -B ${data_dir}:/app/data /home/faird/shared/projects/BME-X/code/bme-x_v1.0.3.sif python /BME-X.py --pretrained_dir /Model --subject_id ${subj_id} --session_id ${ses_id} --bids_root test --roi_x 64 --roi_y 64 --roi_z 64 --N4 False

[lundq163]

tagging @ericfeczko for reference