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danjgale / nii-masker

Convenient command-line wrapper for nilearn's Masker objects
BSD 3-Clause "New" or "Revised" License
7 stars 3 forks source link

Support for NiftiMapsMasker #3

Closed danjgale closed 5 years ago

danjgale commented 5 years ago

Right now niimasker extracts data via NiftiMasker or NiftiLabelsMasker, which assumes that each voxel has a single region assignment (value). nilearn has several probabilistic atlases which can be used with NiftiMapsMasker. So, this enhancement is dependent on #1, and would be a great follow-up to that upon completion.

danjgale commented 5 years ago

Turns out adding probabilistic atlases is not as simple as using NiftiMapsMasker. 4D probabilistic atlases from nilearn add several extra parameters and some API changes that complicate, rather than simplify, the process and code. Because 4D probabilistic atlases are so user-specific, niimasker will focus on labelled deterministic atlases (3D). Therefore, probabilistic atlases must be first thresholded and converted to a 3D image with appropriate labels.