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ReubenDo / MRIPreprocessor

Apache License 2.0
15 stars 3 forks source link

add bet=True to run_hd_bet so that it saves the actual files as well #4

Closed inikishev closed 4 months ago

inikishev commented 4 months ago

change

run_hd_bet(ref_co, ref_sk, mode="fast", device=self.device, do_tta=False)

into

run_hd_bet(ref_co, ref_sk, mode="fast", device=self.device, do_tta=False, bet=True)

which fixes this error

RuntimeError: Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:97:
sitk::ERROR: The file "/mnt/d/vkr/new/nii_preprocessed/skullstripping/patient001_T1.nii.gz" does not exist.