Region image generation

Generates an image of specified Allen institute brain regions (either solid, or hollow).

cellfinder_gen_region_vol -s "Name of Structure 1" "Name of Structure 2" -a /path/to/atlas/annotations.nii -o output.nii

Arguments

Run cellfinder_gen_region_vol -h to see all options.

  • -s or --structure-names Structure names as a series of string (as per the reference atlas). If these are higher level structures (e.g. “Retrosplenial area”), it will include all subregions. If multiple structures are provided the final image will be the combination of all of them.

  • -a or --atlas Path to the atlas annotations. The resulting image will be in the same coordinate space

  • -o or --output Output name for the resulting .nii file

The following options may also need to be used:

  • --glass Generate a hollow volume

  • --atlas-config To supply your own, custom atlas configuration file