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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

Ability to pass multiple atlases/region images #10

Closed danjgale closed 5 years ago

danjgale commented 5 years ago

Currently niimasker only takes one image for mask_img. Users may want to apply several atlases to their data, or in the case of ROIs, several binary masks (which is typical when doing voxel-wise ROI analysis, e.g., MVPA). Rather than calling niimasker several times, a list of nifti images could be provided as input.

danjgale commented 5 years ago

Just realized this gets super messy in a few different ways. 1) If you pass multiple atlases, and want to include labels for each atlas, how do you configure multiple atlas-label pairs in the configuration file (or dare do this via the command line...) 2) You generally want separate output directories for separate atlases – this is not possible if you include multiple atlases.

Although an argument could be made that you could implement this for single ROI images (binary masks) only, but this would be inconsistent with everything else so I'd prefer to just leave things as is.

Perhaps a good substitute for all of this is a good example of a multi-ROI/atlas use-case in the documentation to show people how to use niimasker over several mask imgs. Closing for now until further consideration