class cortex.database.Database[source]

Surface database

This database object dynamically generates handles to all subjects within the filestore.



Initialize self.

clear_cache(subject[, clear_all_caches])

Clears config-specified and default file caches for a subject.

get_anat(subject[, type, xfmname, recache, …])

Return anatomical information from the filestore.


get_coords(subject, xfmname[, hemisphere, …])

Calculate the coordinates of each vertex in the epi space by transforming the fiducial to the coordinate space

get_mask(subject, xfmname[, type])

get_mnixfm(subject, xfm[, template])

Get transform from the space specified by xfm to MNI space.

get_mri_surf2surf_matrix(subject, surface_type)

Get matrix generated by surf2surf to map one subject’s surface to another’s

get_overlay(subject[, overlay_file])


Get a dictionary with a list of all candidate filenames for associated data, such as roi overlays, flatmap caches, and ctm caches.

get_shared_voxels(subject, xfmname[, hemi, …])

Get an array indicating which vertices are inappropriately mapped to the same voxel.

get_surf(subject, type[, hemisphere, merge, …])

Return the surface pair for the given subject, surface type, and hemisphere.

get_surfinfo(subject[, type, recache])

Return auxillary surface information from the filestore.

get_view(vw, subject, name)

Set the view for an open webshow instance from a saved view

get_xfm(subject, name[, xfmtype])

Retrieves a transform from the filestore


save_mask(subject, xfmname, type, mask)

save_view(vw, subject, name[, is_overwrite])

Set the view for an open webshow instance from a saved view

save_xfm(subject, name, xfm[, xfmtype, …])

Load a transform into the surface database.