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