omni.pipelines.anat.masks#
Functions
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Generate an anatomical weight mask |
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Generate an anatomical weight mask (improved version) and autobox the images. |
- omni.pipelines.anat.masks.weight_mask_and_autobox(output_path: str, t1_debias: str, t2_debias: str, anat_bet_mask: str, anat_eye_mask: str, dilation_size: int = 30)[source]#
Generate an anatomical weight mask
- Parameters:
- output_pathstr
Output path to write out files to
- t1_debiasstr
T1 image.
- t2_debiasstr
T2 image.
- anat_bet_maskstr
Anatomical brain mask
- anat_eye_maskstr
Anatomical eye mask
- dilation_sizeint
Dilation size for the weight mask
- Returns:
- str
Weight mask
- str
Weight mask + autobox
- str
Brain mask + autobox
- str
Debiased T1 + autobox
- str
Debiased T2 + autobox
- str
Debiased T1 + autobox + sat/lce
- str
Debiased T2 + autobox + sat/lce
- str
Debiased T1 + autobox + sat/lce + bet
- str
Debiased T2 + autobox + sat/lce + bet
- omni.pipelines.anat.masks.weight_mask_and_autobox2(output_path: str, t1_debias: str, t2_debias: str, anat_bet_mask: str, anat_eye_mask: str, dilation_size: int = 15)[source]#
Generate an anatomical weight mask (improved version) and autobox the images.
- Parameters:
- output_pathstr
Output path to write out files to
- t1_debiasstr
T1 image.
- t2_debiasstr
T2 image.
- anat_bet_maskstr
Anatomical brain mask
- anat_eye_maskstr
Anatomical eye mask
- dilation_sizeint
Dilation size for the weight mask
- Returns:
- str
Weight mask
- str
Weight mask + autobox
- str
Brain mask + autobox
- str
Debiased T1 + autobox
- str
Debiased T2 + autobox
- str
Debiased T1 + autobox + sat/lce
- str
Debiased T2 + autobox + sat/lce
- str
Debiased T1 + autobox + sat/lce + bet
- str
Debiased T2 + autobox + sat/lce + bet