Index

_

__init__() (mcot.core._scripts.cifti.correlate.FakeDConn method) (mcot.core._scripts.cifti.correlate.FakeDConnDataObject method) (mcot.core.greyordinate.GreyOrdinates method)

A

add_to_parser() (in module mcot.core._scripts.cifti.convert) (in module mcot.core._scripts.cifti.correlate) (in module mcot.core._scripts.cifti.ptx2dconn) (in module mcot.core._scripts.cifti.smooth) (in module mcot.core._scripts.function.normalize) (in module mcot.core._scripts.iter_link) (in module mcot.core._scripts.merge_hcp) (in module mcot.core._scripts.parcel.cluster) (in module mcot.core._scripts.parcel.combine) (in module mcot.core._scripts.parcel.discretise) (in module mcot.core._scripts.parcel.random) (in module mcot.core._scripts.parcel.spectral) (in module mcot.core._scripts.ptx.select_vertex) (in module mcot.core._scripts.round_bvals) (in module mcot.core._scripts.split.merge) (in module mcot.core._scripts.split.submit) (in module mcot.core._scripts.surface.from_mask) (in module mcot.core._scripts.surface.from_ridge) (in module mcot.core._scripts.surface.gradient) (in module mcot.core._scripts.surface.roi_dist_gifti) (in module mcot.core._scripts.surface.smooth) (in module mcot.core._scripts.surface.watershed) (in module mcot.core._scripts.to_dataframe) (in module mcot.core._scripts.to_dataframe_tree) (in module mcot.core._scripts.tree.extract)

as_dask() (mcot.core.greyordinate.GreyOrdinates method) axis_from_hdf5() (in module mcot.core.cifti) axis_to_hdf5() (in module mcot.core.cifti)

C

calc_distance() (in module mcot.core._scripts.parcel.random) cart2spherical() (in module mcot.core.spherical) clean_euler() (in module mcot.core.spherical) cluster() (in module mcot.core._scripts.parcel.cluster) combine() (in module mcot.core.cifti)

concatenate() (in module mcot.core.greyordinate) convert_filenames() (in module mcot.core._scripts.to_dataframe) copy() (in module mcot.core._scripts.cifti.convert) correct_type() (in module mcot.core._write_gifti) correlate() (in module mcot.core._scripts.cifti.correlate) correlate_arr() (in module mcot.core._scripts.cifti.correlate)

D

dataframe_to_array() (in module mcot.core._scripts.to_dataframe)

distance() (in module mcot.core._scripts.surface.gradient) dot2matrix() (in module mcot.core._scripts.cifti.ptx2dconn)

E

empty() (mcot.core.greyordinate.GreyOrdinates class method) empty_cifti() (mcot.core.greyordinate.GreyOrdinates class method) empty_hdf5() (in module mcot.core.cifti) (mcot.core.greyordinate.GreyOrdinates class method)

empty_zarr() (in module mcot.core.cifti) (mcot.core.greyordinate.GreyOrdinates class method) euler2mat() (in module mcot.core.spherical)

F

FakeDConn (class in mcot.core._scripts.cifti.correlate) FakeDConnDataObject (class in mcot.core._scripts.cifti.correlate) from_cifti() (in module mcot.core._scripts.to_dataframe) (mcot.core.greyordinate.GreyOrdinates class method) from_filename() (mcot.core.greyordinate.GreyOrdinates class method)

from_gifti() (in module mcot.core._scripts.to_dataframe) (mcot.core.greyordinate.GreyOrdinates class method) from_hdf5() (in module mcot.core.cifti) (mcot.core.greyordinate.GreyOrdinates class method) from_nifti() (in module mcot.core._scripts.to_dataframe) (mcot.core.greyordinate.GreyOrdinates class method)

G

get_brain_model() (in module mcot.core._scripts.cifti.ptx2dconn) get_docstring() (in module mcot.core.scripts) get_job_name() (in module mcot.core._scripts.split.submit) get_level() (in module mcot.core.log)

get_markers() (in module mcot.core._scripts.split.run) get_names() (in module mcot.core._scripts.split.submit) greyordinate_in() (in module mcot.core.scripts) GreyOrdinates (class in mcot.core.greyordinate) guess_extension() (in module mcot.core.cifti)

H

HCP_dir() (in module mcot.core._scripts.merge_hcp)

I

init_center() (in module mcot.core._scripts.parcel.random)

init_random() (in module mcot.core._scripts.parcel.random)

K

kmedoids() (in module mcot.core._scripts.parcel.random)

L

link() (in module mcot.core._scripts.merge_hcp) link_dir() (in module mcot.core._scripts.iter_link)

load_all_mcot() (in module mcot.core.scripts) log_function() (in module mcot.core.log)

M

main() (in module mcot.core._scripts.gcoord.gen) (in module mcot.core._scripts.gcoord.mult) (in module mcot.core._scripts.gcoord.split) (in module mcot.core._scripts.gcoord.transition) (in module mcot.core._scripts.split.run) mat2euler() (in module mcot.core.spherical) mcot.core (module) mcot.core._scripts (module) mcot.core._scripts.cifti.convert (module) mcot.core._scripts.cifti.correlate (module) mcot.core._scripts.cifti.ptx2dconn (module) mcot.core._scripts.cifti.smooth (module) mcot.core._scripts.function.normalize (module) mcot.core._scripts.gcoord.gen (module) mcot.core._scripts.gcoord.mult (module) mcot.core._scripts.gcoord.split (module) mcot.core._scripts.gcoord.transition (module) mcot.core._scripts.iter_link (module) mcot.core._scripts.merge_hcp (module) mcot.core._scripts.parcel.cluster (module) mcot.core._scripts.parcel.combine (module) mcot.core._scripts.parcel.discretise (module) mcot.core._scripts.parcel.random (module) mcot.core._scripts.parcel.spectral (module)

mcot.core._scripts.ptx.select_vertex (module) mcot.core._scripts.round_bvals (module) mcot.core._scripts.split.merge (module) mcot.core._scripts.split.run (module) mcot.core._scripts.split.submit (module) mcot.core._scripts.surface.from_mask (module) mcot.core._scripts.surface.from_ridge (module) mcot.core._scripts.surface.gradient (module) mcot.core._scripts.surface.roi_dist_gifti (module) mcot.core._scripts.surface.smooth (module) mcot.core._scripts.surface.watershed (module) mcot.core._scripts.to_dataframe (module) mcot.core._scripts.to_dataframe_tree (module) mcot.core._scripts.tree.extract (module) mcot.core._write_gifti (module) mcot.core.cifti (module) mcot.core.greyordinate (module) mcot.core.log (module) mcot.core.scripts (module) mcot.core.spherical (module) merge_basenames() (in module mcot.core._scripts.split.merge) merge_directories() (in module mcot.core._scripts.split.merge) merge_files() (in module mcot.core._scripts.split.merge) merge_hcp() (in module mcot.core._scripts.merge_hcp)

O

output() (in module mcot.core.scripts)

P

parse_args() (in module mcot.core._scripts.split.run)

parse_greyordinate() (in module mcot.core.greyordinate)

R

read_ascii() (in module mcot.core._scripts.cifti.ptx2dconn) reduce() (in module mcot.core._scripts.surface.gradient) run() (in module mcot.core._scripts.cifti.correlate) (in module mcot.core._scripts.cifti.ptx2dconn) (in module mcot.core._scripts.function.normalize) (in module mcot.core._scripts.parcel.cluster) (in module mcot.core._scripts.parcel.combine) (in module mcot.core._scripts.parcel.random) (in module mcot.core._scripts.parcel.spectral) (in module mcot.core._scripts.round_bvals) (in module mcot.core._scripts.split.merge) (in module mcot.core._scripts.split.run) (in module mcot.core._scripts.split.submit) (in module mcot.core._scripts.surface.from_mask) (in module mcot.core._scripts.surface.from_ridge) (in module mcot.core._scripts.surface.gradient) (in module mcot.core._scripts.surface.roi_dist_gifti) (in module mcot.core._scripts.surface.watershed) (in module mcot.core._scripts.to_dataframe_tree) (in module mcot.core.scripts) run_array() (in module mcot.core._scripts.parcel.discretise) run_from_args() (in module mcot.core._scripts.cifti.convert) (in module mcot.core._scripts.cifti.correlate) (in module mcot.core._scripts.cifti.ptx2dconn) (in module mcot.core._scripts.cifti.smooth) (in module mcot.core._scripts.function.normalize) (in module mcot.core._scripts.iter_link) (in module mcot.core._scripts.merge_hcp) (in module mcot.core._scripts.parcel.cluster) (in module mcot.core._scripts.parcel.combine) (in module mcot.core._scripts.parcel.discretise) (in module mcot.core._scripts.parcel.random) (in module mcot.core._scripts.parcel.spectral) (in module mcot.core._scripts.ptx.select_vertex) (in module mcot.core._scripts.round_bvals) (in module mcot.core._scripts.split.merge) (in module mcot.core._scripts.split.submit) (in module mcot.core._scripts.surface.from_mask) (in module mcot.core._scripts.surface.from_ridge) (in module mcot.core._scripts.surface.gradient) (in module mcot.core._scripts.surface.roi_dist_gifti) (in module mcot.core._scripts.surface.smooth) (in module mcot.core._scripts.surface.watershed) (in module mcot.core._scripts.to_dataframe) (in module mcot.core._scripts.to_dataframe_tree) (in module mcot.core._scripts.tree.extract)

run_nparcels() (in module mcot.core._scripts.surface.watershed) run_script() (in module mcot.core.scripts)

S

setup_log() (in module mcot.core.log) single_rotmat() (in module mcot.core.spherical) smooth() (in module mcot.core._scripts.cifti.smooth) smooth_cifti() (in module mcot.core._scripts.cifti.smooth) sparse_min() (in module mcot.core._scripts.surface.roi_dist_gifti)

spherical2cart() (in module mcot.core.spherical) stack() (in module mcot.core.greyordinate) surface() (mcot.core.greyordinate.GreyOrdinates method) surface_arr_in() (in module mcot.core.scripts) surface_in() (in module mcot.core.scripts) surface_label_in() (in module mcot.core.scripts)

T

to_cifti() (mcot.core.greyordinate.GreyOrdinates method) to_filename() (mcot.core.greyordinate.GreyOrdinates method) to_hdf5() (in module mcot.core.cifti) (mcot.core.greyordinate.GreyOrdinates method)

to_nifti() (in module mcot.core._scripts.to_dataframe) transpose() (mcot.core.greyordinate.GreyOrdinates method)

U

uniform_centroids() (in module mcot.core._scripts.parcel.random) update_centers() (in module mcot.core._scripts.parcel.random)

update_labels() (in module mcot.core._scripts.parcel.random) usage() (in module mcot.core._scripts.split.run)

V

volume() (mcot.core.greyordinate.GreyOrdinates method)

volume_in() (in module mcot.core.scripts)

W

write() (in module mcot.core.cifti)

write_gifti() (in module mcot.core._write_gifti)