Index

_

__init__() (mcot.bibtex.entry.Author method) (mcot.bibtex.entry.BibTexEntry method) (mcot.bibtex.file.BibTexFile method) (mcot.bibtex.file.BibTexSet method) (mcot.cifti.greyordinate.GreyOrdinates method) (mcot.dippi.geometry.cylinders.PackedCylinders method) (mcot.dippi.model.Model method) (mcot.dippi.model.Parameters method) (mcot.dippi.model.ShellParams method) (mcot.dippi.scan.Encoding method) (mcot.dippi.scan.MultiShell method) (mcot.dippi.scan.ObservedShell method) (mcot.dippi.scan.Scanner method) (mcot.dippi.scan.SimulatedShell method) (mcot.dippi.simulator.FibrePopulation method) (mcot.gcoord.orientation.WeightedOrientation method) (mcot.mde.xps.AcquisitionParams method) (mcot.org.database.ExternalLink method) (mcot.org.database.RoamFile method) (mcot.org.database.RoamNode method) (mcot.surface.cortex.Cortex method) (mcot.surface.cortex.CorticalLayer method) (mcot.surface.cortical_mesh.BrainStructure method) (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.grid.GridSurfaceIntersection method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) (mcot.surface.mesh.ProjectedMesh method) (mcot.utils.scripts.ScriptDirectories method)

A

AcquisitionParams (class in mcot.mde.xps) add() (mcot.bibtex.file.BibTexFile method) (mcot.bibtex.file.BibTexSet method) (mcot.utils.scripts.ScriptDirectories method) add_to_file() (mcot.bibtex.file.BibTexFile method) add_traits() (mcot.bibtex.entry.BibTexEntry method) adjust_id() (mcot.bibtex.entry.BibTexEntry method) affine_mult() (in module mcot.surface.utils) align_vector_field() (in module mcot.gcoord.orientation) alignment() (in module mcot.dippi.model) all_scripts() (mcot.utils.scripts.ScriptDirectories method) angle2bvec() (in module mcot.mde.xps) angle2fullrot() (in module mcot.mde.xps) apply_affine() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method)

as_dask() (mcot.cifti.greyordinate.GreyOrdinates method) as_dict() (mcot.dippi.simulator.FibrePopulation method) as_lines() (mcot.surface.mesh.Mesh1D method) as_temp_file() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) Author (class in mcot.bibtex.entry) auto_update() (mcot.mde.xps.AcquisitionParams method) average_line_grid() (mcot.gcoord.orientation.WeightedOrientation method) average_line_vox() (mcot.gcoord.orientation.WeightedOrientation method) average_orientation() (in module mcot.surface.utils) average_point() (mcot.gcoord.orientation.WeightedOrientation method) average_point_grid() (mcot.gcoord.orientation.WeightedOrientation method) axis_from_hdf5() (in module mcot.cifti.cifti) axis_to_hdf5() (in module mcot.cifti.cifti)

B

BibTexEntry (class in mcot.bibtex.entry) BibTexFile (class in mcot.bibtex.file) BibTexSet (class in mcot.bibtex.file) biorxiv_to_doi() (in module mcot.bibtex.pubmed) bounding() (in module mcot.surface.grid)

BrainStructure (class in mcot.surface.cortical_mesh) bt2b() (in module mcot.mde.xps) bt2btensor() (in module mcot.mde.xps) btensor2bt() (in module mcot.mde.xps) bvec2angle() (in module mcot.mde.xps)

C

cart2spherical() (in module mcot.utils.maths.spherical) check() (mcot.mde.xps.AcquisitionParams method) check_complete() (mcot.bibtex.entry.BibTexEntry method) check_field_text_finished() (in module mcot.bibtex.file) cite_text() (mcot.bibtex.entry.BibTexEntry method) class_own_trait_events() (mcot.bibtex.entry.BibTexEntry class method) class_own_traits() (mcot.bibtex.entry.BibTexEntry class method) class_trait_names() (mcot.bibtex.entry.BibTexEntry class method) class_traits() (mcot.bibtex.entry.BibTexEntry class method) clean() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) clean_euler() (in module mcot.utils.maths.spherical) clear() (mcot.mde.xps.AcquisitionParams method) closed() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) closest_point() (in module mcot.surface.grid) closest_surface() (in module mcot.surface.grid)

closest_vertex() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) closest_vertex_grid() (mcot.gcoord.orientation.WeightedOrientation method) combine() (in module mcot.cifti.cifti) concat() (in module mcot.mde.xps) concatenate() (in module mcot.cifti.greyordinate) connected_components() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) copy() (mcot.dippi.model.Parameters method) (mcot.mde.xps.AcquisitionParams method) Cortex (class in mcot.surface.cortex) CorticalLayer (class in mcot.surface.cortex) CorticalMesh (class in mcot.surface.cortical_mesh) cost() (mcot.dippi.model.Model method) create_spherical_cortex() (in module mcot.surface.test_data)

D

decompose() (in module mcot.mde.xps) default_database() (in module mcot.org.database) default_dependencies() (in module mcot.dippi.model)

derivative() (mcot.dippi.model.Model method) distance() (mcot.surface.cortex.Cortex method) doi_to_bibtex() (in module mcot.bibtex.pubmed)

E

eddy_gradient() (in module mcot.dippi.model) edge_intersect() (mcot.surface.grid.GridSurfaceIntersection method) eigenvalues2shape() (in module mcot.mde.xps) empty() (mcot.cifti.greyordinate.GreyOrdinates class method) (mcot.dippi.model.Parameters class method) empty_cifti() (mcot.cifti.greyordinate.GreyOrdinates class method) empty_hdf5() (in module mcot.cifti.cifti) (mcot.cifti.greyordinate.GreyOrdinates class method)

empty_zarr() (in module mcot.cifti.cifti) (mcot.cifti.greyordinate.GreyOrdinates class method) Encoding (class in mcot.dippi.scan) enumerated() (mcot.dippi.scan.MultiShell method) estimate_eddy() (in module mcot.dippi.model) euler2mat() (in module mcot.utils.maths.spherical) external_phase() (mcot.dippi.geometry.cylinders.PackedCylinders method) ExternalLink (class in mcot.org.database) extract_ridge_values() (in module mcot.surface.track)

F

FibrePopulation (class in mcot.dippi.simulator) fig_plotly() (in module mcot.org.network) find_intersections() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) finish_text() (in module mcot.bibtex.file) fit() (in module mcot.dippi.model) flatten_gradient() (in module mcot.surface.track) format_author() (in module mcot.bibtex.pubmed) from_bedpostx() (mcot.dippi.model.Parameters class method) from_cifti() (mcot.cifti.greyordinate.GreyOrdinates class method) from_dict() (mcot.dippi.model.Parameters class method) (mcot.dippi.scan.ObservedShell class method) (mcot.dippi.scan.Scanner class method) (mcot.dippi.scan.SimulatedShell class method) from_filename() (mcot.cifti.greyordinate.GreyOrdinates class method) from_gifti() (mcot.cifti.greyordinate.GreyOrdinates class method)

from_hdf5() (in module mcot.cifti.cifti) (mcot.cifti.greyordinate.GreyOrdinates class method) from_json() (mcot.dippi.scan.MultiShell class method) (mcot.dippi.scan.ObservedShell class method) (mcot.dippi.scan.Scanner class method) (mcot.dippi.scan.SimulatedShell class method) (mcot.mde.xps.AcquisitionParams class method) from_list() (mcot.dippi.scan.MultiShell class method) from_mat() (mcot.mde.xps.AcquisitionParams class method) from_nifti() (mcot.cifti.greyordinate.GreyOrdinates class method) from_pandas() (mcot.mde.xps.AcquisitionParams class method) from_string() (mcot.bibtex.file.BibTexFile static method) (mcot.bibtex.file.BibTexSet static method) (mcot.surface.cortical_mesh.BrainStructure class method) fromkeys() (mcot.mde.xps.AcquisitionParams method) fullrot2angle() (in module mcot.mde.xps) func_args() (mcot.dippi.model.Model method)

G

gcoord_mult() (in module mcot.surface.utils) gcoord_split() (in module mcot.surface.utils) get() (mcot.bibtex.entry.BibTexEntry method) (mcot.mde.xps.AcquisitionParams method) get_bounds() (in module mcot.dippi.model) get_brain_structure() (in module mcot.surface.cortical_mesh) get_cost() (mcot.dippi.model.Model method) get_docstring() (in module mcot.utils.scripts) get_equations() (mcot.dippi.model.Model method) get_fetcher() (in module mcot.bibtex.pubmed) get_firefox() (in module mcot.bibtex.pubmed) get_func() (mcot.dippi.model.Model method) get_graph() (in module mcot.org.network) get_index() (mcot.mde.xps.AcquisitionParams method) get_level() (in module mcot.utils.log) get_sidecar() (in module mcot.mde.xps) global_fit() (in module mcot.dippi.model) gradient() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method)

graph_connection_connection() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) graph_connection_point() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) graph_point_point() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) greyordinate_in() (in module mcot.cifti.cmd) GreyOrdinates (class in mcot.cifti.greyordinate) GridSurfaceIntersection (class in mcot.surface.grid) groupby() (mcot.mde.xps.AcquisitionParams method) guess_extension() (in module mcot.cifti.cifti) guess_orient() (mcot.dippi.model.Parameters method) gyral_bias() (mcot.surface.cortex.Cortex method)

H

has_trait() (mcot.bibtex.entry.BibTexEntry method)

hold_trait_notifications() (mcot.bibtex.entry.BibTexEntry method)

I

in_axon() (mcot.dippi.geometry.cylinders.PackedCylinders method) inflate() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) intersect() (in module mcot.surface.grid)

intersect_resolution() (in module mcot.surface.grid) intra_axonal_frequency() (mcot.dippi.scan.Scanner method) items() (mcot.dippi.model.ShellParams method) (mcot.mde.xps.AcquisitionParams method)

K

keys() (mcot.bibtex.file.BibTexFile method) (mcot.bibtex.file.BibTexSet method) (mcot.mde.xps.AcquisitionParams method)

L

line_collection() (mcot.surface.mesh.ProjectedMesh method) load() (in module mcot.org.database)

load_all_mcot() (in module mcot.utils.scripts) load_info() (in module mcot.utils.build)

M

make_perpendicular() (in module mcot.gcoord.orientation) mat2euler() (in module mcot.utils.maths.spherical) mcot.bibtex module mcot.bibtex.arxiv module mcot.bibtex.entry module mcot.bibtex.file module mcot.bibtex.pubmed module mcot.cifti module mcot.cifti.cifti module mcot.cifti.cmd module mcot.cifti.greyordinate module mcot.dippi module mcot.dippi.geometry module mcot.dippi.geometry.cylinders module mcot.dippi.model module mcot.dippi.scan module mcot.dippi.simulator module mcot.gcoord module mcot.gcoord.orientation module mcot.mde module mcot.mde.xps module mcot.org module mcot.org.database module mcot.org.network module mcot.surface module mcot.surface.all module mcot.surface.cortex module mcot.surface.cortical_mesh module mcot.surface.grid module mcot.surface.mesh module mcot.surface.test_data module mcot.surface.track module

mcot.surface.utils module mcot.utils module mcot.utils.build module mcot.utils.log module mcot.utils.maths module mcot.utils.maths.spherical module mcot.utils.scripts module Mesh (class in mcot.surface.mesh) Mesh1D (class in mcot.surface.mesh) Mesh2D (class in mcot.surface.mesh) mesh_to_cortex() (in module mcot.surface.test_data) Model (class in mcot.dippi.model) model_signal() (in module mcot.dippi.simulator) module mcot.bibtex mcot.bibtex.arxiv mcot.bibtex.entry mcot.bibtex.file mcot.bibtex.pubmed mcot.cifti mcot.cifti.cifti mcot.cifti.cmd mcot.cifti.greyordinate mcot.dippi mcot.dippi.geometry mcot.dippi.geometry.cylinders mcot.dippi.model mcot.dippi.scan mcot.dippi.simulator mcot.gcoord mcot.gcoord.orientation mcot.mde mcot.mde.xps mcot.org mcot.org.database mcot.org.network mcot.surface mcot.surface.all mcot.surface.cortex mcot.surface.cortical_mesh mcot.surface.grid mcot.surface.mesh mcot.surface.test_data mcot.surface.track mcot.surface.utils mcot.utils mcot.utils.build mcot.utils.log mcot.utils.maths mcot.utils.maths.spherical mcot.utils.scripts MultiShell (class in mcot.dippi.scan) myelin_phase() (in module mcot.dippi.model)

N

neighbour_faces() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) nhit() (mcot.surface.grid.GridSurfaceIntersection method)

normal() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) notify_change() (mcot.bibtex.entry.BibTexEntry method)

O

observe() (mcot.bibtex.entry.BibTexEntry method) ObservedShell (class in mcot.dippi.scan)

on_trait_change() (mcot.bibtex.entry.BibTexEntry method) output() (in module mcot.cifti.cmd)

P

PackedCylinders (class in mcot.dippi.geometry.cylinders) Parameters (class in mcot.dippi.model) parse() (mcot.bibtex.entry.Author class method) parse_greyordinate() (in module mcot.cifti.greyordinate) phase_shift() (in module mcot.dippi.simulator)

plane_projection() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) pmid_from_doi() (in module mcot.bibtex.pubmed) pop() (mcot.mde.xps.AcquisitionParams method) popitem() (mcot.mde.xps.AcquisitionParams method) ProjectedMesh (class in mcot.surface.mesh)

Q

query_mult() (in module mcot.bibtex.arxiv) (in module mcot.bibtex.pubmed)

R

random_confounds() (in module mcot.dippi.simulator) (mcot.dippi.model.Parameters method) random_eddy_params() (in module mcot.dippi.simulator) ray_intersect() (mcot.surface.grid.GridSurfaceIntersection method) read() (mcot.mde.xps.AcquisitionParams class method) (mcot.surface.cortical_mesh.CorticalMesh class method) (mcot.surface.mesh.Mesh2D class method) read_bvals_bvecs() (mcot.mde.xps.AcquisitionParams class method) read_fsaverage_cortex() (in module mcot.surface.test_data) read_fsaverage_surface() (in module mcot.surface.test_data) read_HCP() (in module mcot.surface.cortex) read_properties() (in module mcot.org.database)

recompute_external_phase() (mcot.dippi.geometry.cylinders.PackedCylinders method) reconstruct() (in module mcot.mde.xps) rectangle() (in module mcot.surface.test_data) register_conversion() (in module mcot.mde.xps) remove() (mcot.bibtex.file.BibTexFile method) (mcot.bibtex.file.BibTexSet method) render() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) RoamFile (class in mcot.org.database) RoamNode (class in mcot.org.database) run() (in module mcot.utils.scripts) run_from_args() (in module mcot.gcoord.orientation) run_script() (in module mcot.utils.scripts)

S

Scanner (class in mcot.dippi.scan) schema() (mcot.dippi.scan.ObservedShell class method) (mcot.dippi.scan.Scanner class method) (mcot.dippi.scan.SimulatedShell class method) ScriptDirectories (class in mcot.utils.scripts) segment() (mcot.surface.cortex.Cortex method) set_population() (mcot.dippi.model.Parameters method) set_trait() (mcot.bibtex.entry.BibTexEntry method) setdefault() (mcot.mde.xps.AcquisitionParams method) setup_instance() (mcot.bibtex.entry.BibTexEntry method) setup_log() (in module mcot.utils.log) ShellParams (class in mcot.dippi.model) show() (in module mcot.org.network) show_pyvis() (in module mcot.org.network) signal() (mcot.dippi.model.Model method) signed_distance() (in module mcot.surface.grid) signed_tetrahedral_volume() (in module mcot.surface.utils) simplify_params() (mcot.dippi.model.Parameters method) SimulatedShell (class in mcot.dippi.scan) simulation_signal() (in module mcot.dippi.simulator) single_fit() (in module mcot.dippi.model) single_rotmat() (in module mcot.utils.maths.spherical) single_shell() (in module mcot.dippi.simulator) size_faces() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method)

size_vertices() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) smooth() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) spanned_coordinates() (mcot.surface.mesh.ProjectedMesh method) sphere() (in module mcot.surface.test_data) spherical2cart() (in module mcot.utils.maths.spherical) spherical_harmonics() (in module mcot.dippi.scan) (mcot.dippi.scan.ObservedShell method) (mcot.dippi.scan.SimulatedShell method) spherical_harmonics_indices() (in module mcot.dippi.scan) split_mask() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) stack() (in module mcot.cifti.greyordinate) stick_magnitude1() (in module mcot.dippi.simulator) stick_signal2() (in module mcot.dippi.simulator) surface() (mcot.cifti.greyordinate.GreyOrdinates method) surface_arr_in() (in module mcot.cifti.cmd) surface_edge_distance() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh method) (mcot.surface.mesh.Mesh1D method) (mcot.surface.mesh.Mesh2D method) surface_in() (in module mcot.cifti.cmd) surface_label_in() (in module mcot.cifti.cmd) surface_step() (in module mcot.surface.track)

T

to_bibtex() (in module mcot.bibtex.arxiv) (in module mcot.bibtex.pubmed) to_change() (mcot.dippi.model.Parameters method) to_cifti() (mcot.cifti.greyordinate.GreyOrdinates method) to_dict() (mcot.dippi.model.Parameters method) (mcot.dippi.scan.ObservedShell method) (mcot.dippi.scan.Scanner method) (mcot.dippi.scan.SimulatedShell method) to_filename() (mcot.cifti.greyordinate.GreyOrdinates method) to_hdf5() (in module mcot.cifti.cifti) (mcot.cifti.greyordinate.GreyOrdinates method) to_json() (mcot.dippi.scan.MultiShell method) (mcot.dippi.scan.ObservedShell method) (mcot.dippi.scan.Scanner method) (mcot.dippi.scan.SimulatedShell method) (mcot.mde.xps.AcquisitionParams method) to_list() (mcot.dippi.scan.MultiShell method) to_mat() (mcot.mde.xps.AcquisitionParams method)

to_pandas() (mcot.mde.xps.AcquisitionParams method) to_vtk_actor() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) to_vtk_mapper() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) to_vtk_polydata() (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method) to_xarray() (mcot.dippi.model.Parameters method) track_to_maximum() (in module mcot.surface.track) trait_defaults() (mcot.bibtex.entry.BibTexEntry method) trait_events() (mcot.bibtex.entry.BibTexEntry class method) trait_has_value() (mcot.bibtex.entry.BibTexEntry method) trait_metadata() (mcot.bibtex.entry.BibTexEntry method) trait_names() (mcot.bibtex.entry.BibTexEntry method) trait_values() (mcot.bibtex.entry.BibTexEntry method) traits() (mcot.bibtex.entry.BibTexEntry method) transpose() (mcot.cifti.greyordinate.GreyOrdinates method) triangle_mesh() (in module mcot.surface.test_data)

U

unobserve() (mcot.bibtex.entry.BibTexEntry method) unobserve_all() (mcot.bibtex.entry.BibTexEntry method) update() (mcot.mde.xps.AcquisitionParams method)

url() (mcot.bibtex.entry.BibTexEntry method) (mcot.org.database.RoamFile method) (mcot.org.database.RoamNode method)

V

values() (mcot.mde.xps.AcquisitionParams method) volume() (mcot.cifti.greyordinate.GreyOrdinates method) (mcot.surface.cortex.Cortex method) (mcot.surface.cortex.CorticalLayer method) (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method)

volume_in() (in module mcot.cifti.cmd)

W

wedge_volume() (mcot.surface.cortex.Cortex method) (mcot.surface.cortex.CorticalLayer method) WeightedOrientation (class in mcot.gcoord.orientation) write() (in module mcot.cifti.cifti) (mcot.bibtex.file.BibTexFile method) (mcot.bibtex.file.BibTexSet method) (mcot.mde.xps.AcquisitionParams method) (mcot.surface.cortical_mesh.CorticalMesh method) (mcot.surface.mesh.Mesh2D method)

write_metric() (mcot.surface.cortical_mesh.CorticalMesh method)