mne.SourceSpaces

class mne.SourceSpaces(source_spaces, info=None)[source]

Represent a list of source space.

Currently implemented as a list of dictionaries containing the source space information

Parameters
source_spaceslist

A list of dictionaries containing the source space information.

infodict

Dictionary with information about the creation of the source space file. Has keys ‘working_dir’ and ‘command_line’.

Attributes
infodict

Dictionary with information about the creation of the source space file. Has keys ‘working_dir’ and ‘command_line’.

Methods

__add__(other)

Combine source spaces.

__contains__(key, /)

Return key in self.

__getitem__(*args, **kwargs)

Get an item.

__iter__(/)

Implement iter(self).

__len__(/)

Return len(self).

__mul__(value, /)

Return self*value.

append(object, /)

Append object to the end of the list.

clear(/)

Remove all items from list.

copy()

Make a copy of the source spaces.

count(value, /)

Return number of occurrences of value.

export_volume(fname[, include_surfaces, …])

Export source spaces to nifti or mgz file.

extend(iterable, /)

Extend list by appending elements from the iterable.

index(value[, start, stop])

Return first index of value.

insert(index, object, /)

Insert object before index.

plot([head, brain, skull, subjects_dir, …])

Plot the source space.

pop([index])

Remove and return item at index (default last).

remove(value, /)

Remove first occurrence of value.

reverse(/)

Reverse IN PLACE.

save(fname[, overwrite])

Save the source spaces to a fif file.

sort(*[, key, reverse])

Sort the list in ascending order and return None.
__add__(other)[source]

Combine source spaces.

__contains__(key, /)

Return key in self.

__getitem__(*args, **kwargs)[source]

Get an item.

__iter__(/)

Implement iter(self).

__len__(/)

Return len(self).

__mul__(value, /)

Return self*value.

append(object, /)

Append object to the end of the list.

clear(/)

Remove all items from list.

copy()[source]

Make a copy of the source spaces.

Returns
srcinstance of SourceSpaces

The copied source spaces.

count(value, /)

Return number of occurrences of value.

export_volume(fname, include_surfaces=True, include_discrete=True, dest='mri', trans=None, mri_resolution=False, use_lut=True, overwrite=False, verbose=None)[source]

Export source spaces to nifti or mgz file.

Parameters
fnamestr

Name of nifti or mgz file to write.

include_surfacesbool

If True, include surface source spaces.

include_discretebool

If True, include discrete source spaces.

dest‘mri’ | ‘surf’

If ‘mri’ the volume is defined in the coordinate system of the original T1 image. If ‘surf’ the coordinate system of the FreeSurfer surface is used (Surface RAS).

transdict, str, or None

Either a transformation filename (usually made using mne_analyze) or an info dict (usually opened using read_trans()). If string, an ending of .fif or .fif.gz will be assumed to be in FIF format, any other ending will be assumed to be a text file with a 4x4 transformation matrix (like the --trans MNE-C option. Must be provided if source spaces are in head coordinates and include_surfaces and mri_resolution are True.

mri_resolutionbool | str

If True, the image is saved in MRI resolution (e.g. 256 x 256 x 256), and each source region (surface or segmentation volume) filled in completely. If “sparse”, only a single voxel in the high-resolution MRI is filled in for each source point.

Changed in version 0.21.0: Support for “sparse” was added.

use_lutbool

If True, assigns a numeric value to each source space that corresponds to a color on the freesurfer lookup table.

overwritebool

If True, overwrite the file if it exists.

New in version 0.19.

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). If used, it should be passed as a keyword-argument only. Defaults to self.verbose.

Notes

This method requires nibabel.

Examples using export_volume:

extend(iterable, /)

Extend list by appending elements from the iterable.

index(value, start=0, stop=sys.maxsize, /)

Return first index of value.

Raises ValueError if the value is not present.

insert(index, object, /)

Insert object before index.

plot(head=False, brain=None, skull=None, subjects_dir=None, trans=None, verbose=None)[source]

Plot the source space.

Parameters
headbool

If True, show head surface.

brainbool | str

If True, show the brain surfaces. Can also be a str for surface type (e.g., ‘pial’, same as True). Default is None, which means ‘white’ for surface source spaces and False otherwise.

skullbool | str | list of str | list of dict | None

Whether to plot skull surface. If string, common choices would be ‘inner_skull’, or ‘outer_skull’. Can also be a list to plot multiple skull surfaces. If a list of dicts, each dict must contain the complete surface info (such as you get from mne.make_bem_model()). True is an alias of ‘outer_skull’. The subjects bem and bem/flash folders are searched for the ‘surf’ files. Defaults to None, which is False for surface source spaces, and True otherwise.

subjects_dirstr | None

Path to SUBJECTS_DIR if it is not set in the environment.

transstr | ‘auto’ | dict | None

The full path to the head<->MRI transform *-trans.fif file produced during coregistration. If trans is None, an identity matrix is assumed. This is only needed when the source space is in head coordinates.

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). If used, it should be passed as a keyword-argument only. Defaults to self.verbose.

Returns
figinstance of mayavi.mlab.Figure

The figure.

Examples using plot:

pop(index=- 1, /)

Remove and return item at index (default last).

Raises IndexError if list is empty or index is out of range.

remove(value, /)

Remove first occurrence of value.

Raises ValueError if the value is not present.

reverse(/)

Reverse IN PLACE.

save(fname, overwrite=False)[source]

Save the source spaces to a fif file.

Parameters
fnamestr

File to write.

overwritebool

If True, the destination file (if it exists) will be overwritten. If False (default), an error will be raised if the file exists.

sort(*, key=None, reverse=False)

Sort the list in ascending order and return None.

The sort is in-place (i.e. the list itself is modified) and stable (i.e. the order of two equal elements is maintained).

If a key function is given, apply it once to each list item and sort them, ascending or descending, according to their function values.

The reverse flag can be set to sort in descending order.