wonambi.attr.anat module

Module to read and return anatomical information, such as: - surfaces, with class Surf - brains, with class BrainSurf (both hemispheres)

class wonambi.attr.anat.Brain(freesurfer_dir, surf_type='pial')[source]

Bases: object

Class that contains the left and right hemispheres.

Parameters:

  • freesurfer_dir (str) – subject-specific directory created by freesurfer

  • surf_type (str) – ‘pial’, ‘smoothwm’, ‘inflated’, ‘white’, or ‘sphere’

class wonambi.attr.anat.Freesurfer(freesurfer_dir, fs_lut=None)[source]

Bases: object

Provide class Freesurfer, with the information from freesurfer.

Parameters:

  • freesurfer_dir (str or Path) – subject-specific directory created by freesurfer

  • fs_lut (str or Path) – path to file called FreeSurferColorLUT.txt

Notes

It’s necessary that Freesurfer is installed and that the environmental variable ‘FREESURFER_HOME’ is present.

find_brain_region(abs_pos, parc_type='aparc', max_approx=None, exclude_regions=None)[source]

Find the name of the brain region in which an electrode is located.

Parameters:

  • abs_pos (numpy.ndarray) – 3x0 vector with the position of interest.

  • parc_type (str) – ‘aparc’, ‘aparc.a2009s’, ‘BA’, ‘BA.thresh’, or ‘aparc.DKTatlas40’ ‘aparc.DKTatlas40’ is only for recent freesurfer versions

  • max_approx (int, optional) – max approximation to define position of the electrode.

  • exclude_regions (list of str or empty list) – do not report regions if they contain these substrings. None means that it does not exclude any region.

Notes

It determines the possible brain region in which one electrode is present, based on Freesurfer segmentation. You can imagine that sometimes one electrode is not perfectly located within one region, but it’s a few mm away. The parameter “approx” specifies this tolerance where each value is one mm. It keeps on searching in larger and larger spots until it finds at least one region which is not white matter. If there are multiple regions, it returns the region with the most detection. Minimal value is 0, which means only if the electrode is in the precise location.

If you want to exclude white matter regions with ‘aparc’, use

exclude_regions = (‘White’, ‘WM’, ‘Unknown’)

and with ‘aparc.a2009s’, use:

exclude_regions = (‘White-Matter’)

read_brain(surf_type='pial')[source]

Read the surface of both hemispheres.

Parameters:

surf_type (str) – ‘pial’, ‘smoothwm’, ‘inflated’, ‘white’, or ‘sphere’

Returns:

instance of Brain – the surfaces of both brain hemispheres

read_label(hemi, parc_type='aparc')[source]

Read the labels (annotations) for each hemisphere.

Parameters:

  • hemi (str) – ‘lh’ or ‘rh’

  • parc_type (str) – ‘aparc’, ‘aparc.a2009s’, ‘BA’, ‘BA.thresh’, or ‘aparc.DKTatlas40’ ‘aparc.DKTatlas40’ is only for recent freesurfer versions

Returns:

  • numpy.ndarray – value at each vertex, indicating the label

  • numpy.ndarray – RGB + alpha colors for each label

  • list of str – names of the labels

read_seg(parc_type='aparc')[source]

Read the MRI segmentation.

Parameters:

parc_type (str) – ‘aparc’ or ‘aparc.a2009s’

Returns:

  • numpy.ndarray – 3d matrix with values

  • numpy.ndarray – 4x4 affine matrix

property surface_ras_shift

one for volumes (“RAS”) and one for surfaces (“tkReg”, “tkRAS”, and “Surface RAS”). To get from surface to volume coordinates, add this numbers. To get from volume to surface coordinates, substract this numbers.

Type:

Freesurfer uses two coordinate systems

class wonambi.attr.anat.Surf(surf_file)[source]

Bases: object

Provide class Surf, with the positions and connections of vertices.

Parameters:

surf_file (str or Path) – freesurfer file containing the surface

surf_file

freesurfer file containing the surface

Type:

path to file

vert

vertices of the mesh

Type:

numpy.ndarray

tri

triangulation of the mesh

Type:

numpy.ndarray

wonambi.attr.anat.import_freesurfer_LUT(fs_lut=None)[source]

Import Look-up Table with colors and labels for anatomical regions.

It’s necessary that Freesurfer is installed and that the environmental variable ‘FREESURFER_HOME’ is present.

Parameters:

fs_lut (str or Path) – path to file called FreeSurferColorLUT.txt

Returns:

  • idx (list of int) – indices of regions

  • label (list of str) – names of the brain regions

  • rgba (numpy.ndarray) – one row is a brain region and the columns are the RGB + alpha colors