class cortex.database.Database[source]

Surface database

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


__init__(self[, filestore])

Initialize self.

clear_cache(self, subject[, clear_all_caches])

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

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

Return anatomical information from the filestore.

get_cache(self, subject)

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

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

get_mask(self, subject, xfmname[, type])

get_mnixfm(self, subject, xfm[, template])

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

get_mri_surf2surf_matrix(self, subject, …)

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

get_overlay(self, subject[, overlay_file])

get_paths(self, subject)

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(self, subject, xfmname[, …])

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

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

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

get_surfinfo(self, subject[, type, recache])

Return auxillary surface information from the filestore.

get_view(self, vw, subject, name)

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

get_xfm(self, subject, name[, xfmtype])

Retrieves a transform from the filestore

make_subj(self, subject)

save_mask(self, subject, xfmname, type, mask)

save_view(self, vw, subject, name[, …])

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

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

Load a transform into the surface database.