Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

5.2.5. sammba.data_fetchers.fetch_masks_dorr_2008

sammba.data_fetchers.fetch_masks_dorr_2008(image_format='nifti', downsample='30', data_dir=None, resume=True, verbose=1)

Downloads DORR 2008 atlas first, then uses its labels to produce tissue masks.

Parameters

image_format : one of {‘nifti’, ‘minc’}, optional

Format to download

downsample : one of {‘30’, ‘100’}, optional

Downsampling resolution in microns.

data_dir : str, optional

Path of the data directory. Use to forec data storage in a non- standard location. Default: None (meaning: default)

resume : bool, optional

whether to resumed download of a partly-downloaded file.

verbose : int, optional

verbosity level (0 means no message).

Returns

mask_imgs: sklearn.datasets.base.Bunch

dictionary-like object, contains:

  • ‘brain’ : nibabel.nifti1.Nifti1Image brain mask image.

  • ‘gm’ : nibabel.nifti1.Nifti1Image grey matter mask image.

  • ‘cc’ : nibabel.nifti1.Nifti1Image eroded corpus callosum mask image.

  • ‘ventricles’nibabel.nifti1.Nifti1Image eroded ventricles mask

    image.

See also

sammba.data_fetchers.fetch_atlas_dorr_2008

for details regarding the DORR 2008 atlas.

Notes

This function relies on DORR 2008 atlas where we particularly pick ventricles and corpus callosum regions. Then, do a bit post processing such as binary closing operation to more compact brain and grey matter mask image and binary erosion to non-contaminated corpus callosum and ventricles mask images. Note: It is advised to check the mask images with your own data processing.