FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/code/coil-qc-code/data-phantom/derivatives/labels/sub-UCL/fmap/sub-UCL_acq-coilQaSagSmall_GFactor_mask.nii.gz'

[jcohenadad]

Version: https://github.com/spinal-cord-7t/coil-qc-code/blob/0609ec86ccd3765fe190344102afdef4f86ecfb7/data_processing-phantom.ipynb

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
File ~/miniconda3/lib/python3.10/site-packages/nibabel/loadsave.py:87, in load(filename, **kwargs)
     86 try:
---> 87     stat_result = os.stat(filename)
     88 except OSError:

FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/code/coil-qc-code/data-phantom/derivatives/labels/sub-UCL/fmap/sub-UCL_acq-coilQaSagSmall_GFactor_mask.nii.gz'

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
Cell In[9], line 14
     11 gfac_data=(gfac_map.get_fdata()[:,:,:,5])
     13 fname_mask=os.path.join(path_labels, subject, "fmap", f"{subject}_acq-coilQaSagSmall_GFactor_mask.nii.gz")
---> 14 gfac_mask_map=nib.load(fname_mask)
     15 gfac_mask_data=(gfac_mask_map.get_fdata()[:,:,:])
     17 # mask data

File ~/miniconda3/lib/python3.10/site-packages/nibabel/loadsave.py:89, in load(filename, **kwargs)
     87     stat_result = os.stat(filename)
     88 except OSError:
---> 89     raise FileNotFoundError(f"No such file or no access: '{filename}'")
     90 if stat_result.st_size <= 0:
     91     raise ImageFileError(f"Empty file: '{filename}'")

FileNotFoundError: No such file or no access: '/Users/julien/code/coil-qc-code/data-phantom/derivatives/labels/sub-UCL/fmap/sub-UCL_acq-coilQaSagSmall_GFactor_mask.nii.gz'

[evaalonsoortiz]

I am no longer using a pre-defined mask, but rather calculating the mean within a central box.