DeepBrainSeg.brainmask package¶

Subpackages¶

DeepBrainSeg.brainmask.antsmask.ANTS_skull_stripping(t1_path, save_path, ants_path)[source]¶

We make use of ants framework for generalized skull stripping

t1_path: t1 volume path (str) saves the mask in the same location as t1 data directory returns: maskvolume (numpy uint8 type)

DeepBrainSeg.brainmask.antsmask.get_ants_mask(ants_path, t1_path)[source]¶

We make use of ants framework for generalized skull stripping

t1_path: t1 volume path (str) saves the mask in the same location as t1 data directory returns: maskvolume (numpy uint8 type)

DeepBrainSeg.brainmask.hdbetmask.bet_skull_stripping(t1_path, save_path)[source]¶

We make use of bet framework for generalized skull stripping

t1_path: t1 volume path (str) saves the mask in the same location as t1 data directory returns: maskvolume (numpy uint8 type)

DeepBrainSeg.brainmask.hdbetmask.get_bet_mask(vol_path, device=0)[source]¶

We make use of bet framework for generalized skull stripping

vol_path: t1 volume path (str) saves the mask in the same location as t1 data directory returns: maskvolume (numpy uint8 type)

DeepBrainSeg.brainmask.get_brain_mask(t1_path, ants_path=None)[source]¶

extracts brain mask, uses ants if ants_path is not none

t1_path: path to t1 nifty image ants_path: build directory of ants