frites.conn.conn_links

frites.conn.conn_links(roi, directed=False, net=False, roi_relation='both', sep='auto', nb_min_links=None, pairs=None, sort=True, triu_k=1, hemisphere=None, hemi_links='both', categories=None, source_seed=None, target_seed=None, verbose=None)

Construct pairwise links for functional connectivity.

This function can be used for defining the pairwise links for computing either undirected or directed FC on M/EEG or intracranial EEG.

Parameters

roinumpy:array_like

List of roi (or contacts) names.

directedbool | python:False

Specify whether the links should be for undirected (False) or directed (True) FC

netbool | python:False

Specify whether it is for net directed FC (True) or not (False)

roi_relation{‘both’, ‘inter’, ‘intra’}

Specify the roi relation between pairs of brain regions. Use either :

• ‘intra’ : to select only links within a brain region (e.g. V1-V1)

• ‘inter’ : to select only links across brain region (e.g. V1-V2)

• ‘both’ : to select links both within and across brain regions

seppython:str | ‘auto’

If ‘auto’, ‘-’ are used to linked brain region names for undirected FC or ‘->’ for directed FC. Alternatively, you can provide a custom separator (e.g. sep=’/’)

nb_min_linkspython:int | python:None

Threshold for defining a minimum number of links between two brain regions (e.g. iEEG)

pairsnumpy:array_like | python:None

Force to use certain pairs of brain regions. Should be an array of shape (n_pairs, 2) where the first column refer to sources and the second to targets

sortbool | python:True

For undirected and net directed FC, sort the names of the brain regions (e.g. ‘V1-M1’ -> ‘M1-V1’)

triu_kpython:int | 1

Diagonal offset when estimating the undirected links to use. By default, triu_k=1 means that we skip auto-connections

hemispherenumpy:array_like | python:None

List of hemisphere names

hemi_links{‘both’, ‘intra’, ‘inter’}

Specify whether connectivity links should be :

• ‘both’: intra-hemispheric and inter-hemispheric (default)

• ‘intra’: intra-hemispheric

• ‘inter’: inter-hemispheric

In order to work, you should provide the hemisphere name using the input hemisphere

categoriesnumpy:array_like | python:list | python:None

Specify categorical information associated to each region to then get links only across categories.

source_seedpython:str, python:list | python:None

Brain region name(s) to use as source seed. Can either be the name of a single brain region or a list of brain regions.

target_seedpython:str, python:list | python:None

Brain region name(s) to use as target seed. Can either be the name of a single brain region or a list of brain regions.

Returns

indicespython:tuple

Remaining indices for (sources, targets)

roi_stpython:list

Name of the pairs of brain regions