visbrain.objects.RoiObj

class visbrain.objects.RoiObj(name, vol=None, labels=None, index=None, hdr=None, system='mni', transform=None, parent=None, verbose=None, preload=True, _scale=1.0, **kw)

Create a Region Of Interest (ROI) object.

Main functionalities

• Display a mesh of selected ROIs

• Localize sources

Supported ROI

• Brodmann Areas

• Talairach atlas

• Automated Anatomical Labeling (AAL)

• MIST, including levels 7, 12, 20, 36, 64, 122 and ROI [1]

Parameters:

namestring

Name of the ROI object. If name is ‘brodmann’, ‘aal’ or ‘talairach’ a predefined ROI object is used and vol, index and label are ignored. MIST [1] is also supported. To specify a resolution use mist_%s with %s in [‘7’, ‘12’, ‘20’, ‘36’, ‘64’, ‘122’, ‘ROI’] (e.g ‘mist_7’, mist_ROI)

volarray_like | None

ROI volume. Sould be an array with three dimensions.

labelsarray_like | None

Array of labels. A structured array can be used (i.e label=np.zeros(n_sources, dtype=[(‘brodmann’, int), (‘aal’, object)])).

indexarray_like | None

Array of index that make the correspondance between the volume values and labels. The length of index must be the same as label.

hdrarray_like | None

Array of transform source’s coordinates into the volume space. Must be a (4, 4) array.

system{‘mni’, ‘tal’}

The system of the volume. Can either be MNI (‘mni’) or Talairach (‘tal’).

transformVisPy.visuals.transforms | None

VisPy transformation to set to the parent node.

parentVisPy.parent | None

ROI object parent.

verbosestring

Verbosity level.

kwdict | {}

Optional arguments are used to control the colorbar (See ColorbarObj).

Notes

List of supported shortcuts :

• s : save the figure

• <delete> : reset camera

References

[1] (1,2)

Urchs, S., Armoza, J., Benhajali, Y., St-Aubin, J., Orban, P., & Bellec, P. (2017). MIST: A multi-resolution parcellation of functional brain networks. MNI Open Research, 1.

Examples

>>> import numpy as np
>>> from visbrain.objects import RoiObj
>>> r = RoiObj('brodmann')
>>> r.select_roi(select=[4, 6, 38], unique_color=True, smooth=7)
>>> r.preview(axis=True)

Methods

__init__(name[, vol, labels, index, hdr, ...])	Init.
animate([step, interval, iterations])	Animate the object.
copy()	Get a copy of the object.
describe_tree()	Tree description.
get_centroids(select)	Get the (x, y, z) coordinates of the center of a ROI.
get_labels([save_to_path])	Get the labels associated with the loaded ROI.
list([file])	Get the list of installed volumes.
localize_sources(xyz[, source_name, ...])	Localize source's using this ROI object.
pos_to_slice(pos[, axis, hdr])	Return the slice from position.
preview([bgcolor, axis, xyz, show, obj, ...])	Previsualize the result.
project_sources(s_obj[, project, radius, ...])	Project source's activity or repartition onto ROI.
record_animation(name[, n_pic, bgcolor])	Record an animated object and save as a *.gif file.
remove()	Remove the volume template.
render()	Render the canvas.
reset()	Reset the RoiObject.
save([tmpfile])	Save the volume template.
screenshot(saveas[, print_size, dpi, unit, ...])	Take a screeshot of the scene.
select_roi([select, unique_color, ...])	Select several Region Of Interest (ROI).
set_data(name[, vol, labels, index, hdr, system])	Load an roi object.
set_shortcuts_to_canvas(canvas)	Set shortcuts to a VisbrainCanvas.
slice_to_pos(sl[, axis, hdr])	Return the position from slice in the volume space.
to_dict()	Return a dictionary of all colorbar args.
to_kwargs([addisminmax])	Return a dictionary for input arguments.
update()	Fonction to run when an update is needed.
update_from_dict(kwargs)	Update attributes from a dictionary.
where_is(patterns[, df, union, columns, ...])	Find a list of string patterns in a DataFrame.

Examples using visbrain.objects.RoiObj

Combine multiple objects

Combine multiple objects

Region Of Interest object (RoiObj) : complete tutorial

Region Of Interest object (RoiObj) : complete tutorial

Source object (SourceObj) : complete tutorial

Source object (SourceObj) : complete tutorial

Add Region of interest (ROI)

Add Region of interest (ROI)

Screenshot example

Screenshot example