Atlas utilities

Includes function to obtain information on standard atlases, coordinates, etc.

sekupy.utils.atlas.find_roi_center(img, roi_value)[source]

This function gives the x,y,z coordinates of a particular ROI using the given segmented image and the image level value used to select the ROI.

Parameters:

  • img (nibabel Nifti1Image instance) – The Nifti1Image instance of the segmented image.

  • roi_value (int) – The value of the ROI as represented in the segmented image

Returns:

xyz – A triplets representing the xyz coordinate of the selected ROI.

Return type:

tuple

sekupy.utils.atlas.get_aal_coords(fname)[source]

Function used to obtain coordinates of the ROIs contained in the AAL90 atlas. The atlas used is the 2mm nifti version of the atlas.

Parameters:

fname (string) – The path of the atlas to be used.

Returns:

coords – The array containing n xyz coordinates in MNI space, one for each unique value of the atlas

Return type:

n x 3 numpy array

sekupy.utils.atlas.get_aalmeg_info(background='black', grouping='LR')[source]

[summary]

Parameters:

  • background (str, optional) – [description], by default ‘black’

  • grouping (str, optional) – [description], by default ‘LR’ or ‘lobes’

Returns:

[description]

Return type:

[type]

sekupy.utils.atlas.get_atlas90_info(background='black')[source]

Utility function used to load informations about the atlas used

Parameters:

background (string | {'black', 'white'}) – A string used to build colors for plots.

Returns:

  • names (list of string) – The list of ROI names.

  • colors (list of string) – The list of colors used in other functions

  • index_ (list of int) – How node values should be ordered if the atlas has another order (used to separate left/right in the atlas90)

  • coords (list of tuple (x,y,z)) – Coordinates of the ROI center (used in plot_connectomics)

  • networks (list of string) – The list of network names.

sekupy.utils.atlas.get_atlas_info(atlas_name='findlab')[source]

This function is used to obtain information on different atlases.

Parameters:

atlas_name (str, optional ('findlab', 'aal_meg', 'atlas90')) – atlas name to get information

Returns:

labels : names of nodes (n_nodes, string array) colors : colors of each node representing some classification node_idx : order of nodes for plot purposes coords : MNI coordinates of nodes networks : name of networks the node belongs to node_angles : angles for circular plot

Return type:

List of informations of the atlas

sekupy.utils.atlas.get_eeg_channels(n_channels=159)[source]
sekupy.utils.atlas.get_findlab_coords()[source]

Function used to obtain coordinates of the networks contained in the findlab atlas. The atlas used is the 2mm nifti version of the atlas.

Returns:

coords – The array containing n xyz coordinates in MNI space, one for each unique value of the atlas

Return type:

n x 3 numpy array

sekupy.utils.atlas.get_findlab_info(background='black')[source]
sekupy.utils.atlas.get_rois_names(path)[source]
sekupy.utils.atlas.get_viviana_info()[source]
sekupy.utils.atlas.where_am_i(fname)[source]

This function is used to find the ROI name in a mask file using AFNI whereami.

Parameters:

fname (string,) – The complete filename of the mask.

Returns:

table – The list has a lenght equal to the number of ROIs contained in the file Elements of the list: (x, y, z): coordinates of ROI’s center of mass. label: name of the brain area closest to the center of mass num: number of voxels included in the ROI value: value of the ROI in the input file

Return type:

list