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Fix mask output filename issues when '.nii.gz' is not included in out_fname #53

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Fix mask output filename issues when '.nii.gz' is not included in out_fname #53

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3 changes: 2 additions & 1 deletion HD_BET/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,8 @@ def run_hd_bet(mri_fnames, output_fnames, mode="accurate", config_file=os.path.j
params.append(torch.load(p, map_location=lambda storage, loc: storage))

for in_fname, out_fname in zip(mri_fnames, output_fnames):
mask_fname = out_fname[:-7] + "_mask.nii.gz"
# mask_fname = out_fname[:-7] + "_mask.nii.gz" # If user doesn't include '.nii.gz' ext, this will cause issues
mask_fname = out_fname.replace('.nii.gz','') + '_mask.nii.gz' # this should work even if out_fname doesn't include .nii.gz ext
if overwrite or (not (os.path.isfile(mask_fname) and keep_mask) or not os.path.isfile(out_fname)):
print("File:", in_fname)
print("preprocessing...")
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