CerebNet.datasets.wm_merge_clean

CerebNet.datasets.wm_merge_clean.add_cereb_wm(cereb_subseg, aseg, manual_cereb)

Adding cerebellar wm from FreeSurfer and filling the gaps if cereb_subseg is dzne_manual we also update FreeSurfer cereb wm accordingly

Parameters:

• cereb_subseg

• aseg

• manual_cereb

Returns:

CerebNet.datasets.wm_merge_clean.cereb_subseg_lateral_mask(cereb_subseg)

Create mask for left and right cerebellar gray matter.

CerebNet.datasets.wm_merge_clean.correct_cereb_brainstem(cereb_subseg, brainstem, manual_cereb)

Correct brainstem or cereb_subseg according to the other (select which to correct by manual_cereb).

CerebNet.datasets.wm_merge_clean.drop_disconnected_component(img_data, classes)

Dropping the smaller disconnected component of each label.

CerebNet.datasets.wm_merge_clean.filling_unknown_labels(segmap, unknown_mask, candidate_lbls)

For each unknown voxel in unknown_mask, find and fill it with a candidate.

CerebNet.datasets.wm_merge_clean.locating_unknowns(gm_binary, wm_mask)

Find labels with missing labels, i.e. find holes.

CerebNet.datasets.wm_merge_clean.save_mgh_image(img_data, save_path, header, affine)

Save data as mgh image.

CerebNet.datasets.wm_merge_clean.sphere(radius)

Create a spherical binary mask.