Index

_

__init__() (cortex.database.Database method) (cortex.dataset.Dataset method) (cortex.dataset.Vertex method) (cortex.dataset.Vertex2D method) (cortex.dataset.VertexRGB method) (cortex.dataset.Volume method) (cortex.dataset.Volume2D method) (cortex.dataset.VolumeRGB method) (cortex.freesurfer.SpringLayout method) (cortex.mapper.Mapper method) (cortex.polyutils.Distortion method) (cortex.polyutils.Surface method) (cortex.xfm.Transform method)

A

add_roi() (in module cortex.utils) adj (cortex.polyutils.Surface property) alpha (cortex.dataset.VertexRGB property) (cortex.dataset.VolumeRGB property) anat2epispace() (in module cortex.utils) (in module cortex.volume) anat2epispace_fsl() (in module cortex.volume)

append() (cortex.dataset.Dataset method) approx_geodesic_distance() (cortex.polyutils.Surface method) areal (cortex.polyutils.Distortion property) automatic() (in module cortex.align) autorecon() (in module cortex.freesurfer) autotweak() (in module cortex.align) avg_edge_length (cortex.polyutils.Surface property)

B

blend_curvature() (cortex.dataset.Vertex method) (cortex.dataset.Vertex2D method) (cortex.dataset.VertexRGB method)

boundary_vertices (cortex.polyutils.Surface property) brainmask() (in module cortex.anat)

C

call_vtp_geodesic() (cortex.polyutils.Surface method) clear_cache() (cortex.database.Database method) color_voxels() (cortex.dataset.VolumeRGB static method) compute_mni_transform() (in module cortex.mni) connected (cortex.polyutils.Surface property) copy() (cortex.dataset.Vertex method) (cortex.dataset.Vertex2D method) (cortex.dataset.VertexRGB method) (cortex.dataset.Volume method) (cortex.dataset.Volume2D method) (cortex.dataset.VolumeRGB method) cortex.align module cortex.anat module cortex.database module cortex.dataset module cortex.freesurfer module cortex.mapper module

cortex.mni module cortex.polyutils module cortex.quickflat module cortex.segment module cortex.surfinfo module cortex.utils module cortex.volume module cortex.webgl module cortex.xfm module cotangent_weights (cortex.polyutils.Surface property) create_biharmonic_solver() (cortex.polyutils.Surface method) create_subsurface() (cortex.polyutils.Surface method) curvature() (in module cortex.surfinfo) cut_surface() (in module cortex.segment)

D

data (cortex.dataset.Vertex property) (cortex.dataset.Volume property) Database (class in cortex.database)

Dataset (class in cortex.dataset) Distortion (class in cortex.polyutils) distortion() (in module cortex.surfinfo)

E

edge_collapse() (cortex.polyutils.Surface method) edge_lengths (cortex.polyutils.Surface property) empty() (cortex.dataset.Vertex class method) (cortex.dataset.Volume class method) epi2anatspace() (in module cortex.volume)

epi2anatspace_fsl() (in module cortex.volume) exact_geodesic_distance() (cortex.polyutils.Surface method) exp() (cortex.dataset.Vertex method) (cortex.dataset.Volume method) extract_chunk() (cortex.polyutils.Surface method) extract_geodesic_chunk() (cortex.polyutils.Surface method)

F

face_areas (cortex.polyutils.Surface property) face_normals (cortex.polyutils.Surface property) fix_pia() (in module cortex.segment) fix_wm() (in module cortex.segment) flat_border() (in module cortex.surfinfo) flatten() (in module cortex.freesurfer) from_file() (cortex.dataset.Dataset class method)

from_hdf() (cortex.dataset.Vertex static method) (cortex.dataset.Vertex2D static method) (cortex.dataset.VertexRGB static method) (cortex.dataset.Volume static method) (cortex.dataset.Volume2D static method) (cortex.dataset.VolumeRGB static method) furthest_border_points (cortex.polyutils.Surface property)

G

geodesic_distance() (cortex.polyutils.Surface method) geodesic_path() (cortex.polyutils.Surface method) get_anat() (cortex.database.Database method) get_aseg_mask() (in module cortex.utils) get_cache() (cortex.database.Database method) get_cmap() (in module cortex.utils) get_cmapdict() (cortex.dataset.Vertex method) (cortex.dataset.Vertex2D method) (cortex.dataset.VertexRGB method) (cortex.dataset.Volume method) (cortex.dataset.Volume2D method) (cortex.dataset.VolumeRGB method) get_connected_vertices() (cortex.polyutils.Surface method) get_coords() (cortex.database.Database method) get_cortical_mask() (in module cortex.utils) get_ctmmap() (in module cortex.utils) get_ctmpack() (in module cortex.utils) get_curv() (in module cortex.freesurfer) get_dropout() (in module cortex.utils) get_euclidean_ball() (cortex.polyutils.Surface method) get_euclidean_patch() (cortex.polyutils.Surface method) get_geodesic_patch() (cortex.polyutils.Surface method) get_geodesic_patches() (cortex.polyutils.Surface method) get_geodesic_strip_patch() (cortex.polyutils.Surface method)

get_graph() (cortex.polyutils.Surface method) get_hemi_masks() (in module cortex.utils) get_mapper() (in module cortex.mapper) get_mask() (cortex.database.Database method) (cortex.dataset.Dataset method) get_mnixfm() (cortex.database.Database method) get_mri_surf2surf_matrix() (cortex.database.Database method) get_overlay() (cortex.database.Database method) (cortex.dataset.Dataset method) get_paths() (cortex.database.Database method) (in module cortex.freesurfer) get_roi_mask() (in module cortex.utils) get_roi_masks() (in module cortex.utils) get_roi_verts() (in module cortex.utils) get_shared_voxels() (cortex.database.Database method) get_strip_coordinates() (cortex.polyutils.Surface method) get_surf() (cortex.database.Database method) (cortex.dataset.Dataset method) (in module cortex.freesurfer) get_surfinfo() (cortex.database.Database method) get_view() (cortex.database.Database method) get_vox_dist() (in module cortex.utils) get_xfm() (cortex.database.Database method) (cortex.dataset.Dataset method) graph (cortex.polyutils.Surface property)

I

import_flat() (in module cortex.freesurfer) import_subj() (in module cortex.freesurfer) init_subject() (in module cortex.segment)

interp() (cortex.polyutils.Surface method) iter_surfedges (cortex.polyutils.Surface property) iter_surfedges_weighted (cortex.polyutils.Surface property)

L

laplace_operator (cortex.polyutils.Surface property) left (cortex.dataset.Vertex property) (cortex.dataset.VertexRGB property)

lift_subsurface_data() (cortex.polyutils.Surface method)

M

make_fiducial() (in module cortex.freesurfer) make_figure() (in module cortex.quickflat) make_movie() (in module cortex.utils) make_png() (in module cortex.quickflat) make_static() (in module cortex.webgl) make_subj() (cortex.database.Database method) make_svg() (in module cortex.quickflat) manual() (in module cortex.align) map() (cortex.dataset.Vertex method) (cortex.dataset.Volume method) Mapper (class in cortex.mapper) mean_curvature() (cortex.polyutils.Surface method) metric (cortex.polyutils.Distortion property) module cortex.align cortex.anat cortex.database cortex.dataset cortex.freesurfer cortex.mapper cortex.mni cortex.polyutils cortex.quickflat cortex.segment cortex.surfinfo cortex.utils cortex.volume cortex.webgl cortex.xfm

mosaic() (in module cortex.volume)

N

name (cortex.dataset.Vertex property) (cortex.dataset.VertexRGB property) (cortex.dataset.Volume property) (cortex.dataset.VolumeRGB property)

P

parse_curv() (in module cortex.freesurfer) parse_patch() (in module cortex.freesurfer) parse_surf() (in module cortex.freesurfer) patches() (cortex.polyutils.Surface method) plot_subsurface_rotating_gif() (cortex.polyutils.Surface method) polyhedra() (cortex.polyutils.Surface method) ppts (cortex.polyutils.Surface property)

prepend() (cortex.dataset.Dataset method) priority (cortex.dataset.Vertex property) (cortex.dataset.Vertex2D property) (cortex.dataset.VertexRGB property) (cortex.dataset.Volume property) (cortex.dataset.Volume2D property) (cortex.dataset.VolumeRGB property)

R

random() (cortex.dataset.Vertex class method) (cortex.dataset.Volume class method) raw (cortex.dataset.Vertex property) (cortex.dataset.Vertex2D property) (cortex.dataset.VertexRGB property) (cortex.dataset.Volume property) (cortex.dataset.Volume2D property) (cortex.dataset.VolumeRGB property)

read_dot() (in module cortex.freesurfer) reload_subjects() (cortex.database.Database method) right (cortex.dataset.Vertex property) (cortex.dataset.VertexRGB property)

S

save() (cortex.dataset.Dataset method) (cortex.dataset.Volume method) save_mask() (cortex.database.Database method) save_nii() (cortex.dataset.Volume method) save_view() (cortex.database.Database method) save_xfm() (cortex.database.Database method) show() (in module cortex.webgl) show_glass() (in module cortex.volume) show_mip() (in module cortex.volume) show_slice() (in module cortex.volume)

show_surf() (in module cortex.freesurfer) smooth() (cortex.polyutils.Surface method) SpringLayout (class in cortex.freesurfer) stretch_mwall() (in module cortex.freesurfer) subject (cortex.dataset.Vertex2D property) (cortex.dataset.Volume2D property) subjects (cortex.database.Database property) subsurface_vertex_inverse (cortex.polyutils.Surface property) Surface (class in cortex.polyutils) surface_gradient() (cortex.polyutils.Surface method)

T

thickness() (in module cortex.surfinfo) tissots_indicatrix() (in module cortex.surfinfo) to_json() (cortex.dataset.Vertex method) (cortex.dataset.Vertex2D method) (cortex.dataset.VertexRGB method) (cortex.dataset.Volume method) (cortex.dataset.Volume2D method) (cortex.dataset.VolumeRGB method)

Transform (class in cortex.xfm) transform_mni_to_subject() (in module cortex.mni) transform_surface_to_mni() (in module cortex.mni) transform_to_mni() (in module cortex.mni)

U

uniques() (cortex.dataset.Dataset method) (cortex.dataset.Vertex method) (cortex.dataset.Vertex2D method) (cortex.dataset.VertexRGB method) (cortex.dataset.Volume method) (cortex.dataset.Volume2D method) (cortex.dataset.VolumeRGB method)

unmask() (in module cortex.volume)

V

Vertex (class in cortex.dataset) Vertex2D (class in cortex.dataset) vertex_normals (cortex.polyutils.Surface property) vertex_to_voxel() (in module cortex.utils) VertexRGB (class in cortex.dataset) vertices (cortex.dataset.Vertex property) (cortex.dataset.Vertex2D property) (cortex.dataset.VertexRGB property)

Volume (class in cortex.dataset) volume (cortex.dataset.Volume property) (cortex.dataset.VolumeRGB property) volume() (cortex.dataset.Vertex method) Volume2D (class in cortex.dataset) VolumeRGB (class in cortex.dataset) voxelize() (in module cortex.anat)

W

weighted_distance_graph (cortex.polyutils.Surface property) whitematter() (in module cortex.anat)

write_decimated() (in module cortex.freesurfer) write_dot() (in module cortex.freesurfer)

X

xfmname (cortex.dataset.Volume2D property)