mne.warp_montage_volume¶

mne.warp_montage_volume(montage, base_image, reg_affine, sdr_morph, subject_from, subject_to='fsaverage', subjects_dir_from=None, subjects_dir_to=None, thresh=0.5, max_peak_dist=1, voxels_max=100, use_min=False, verbose=None)[source]¶

Warp a montage to a template with image volumes using SDR.

Find areas of the input volume with intensity greater than a threshold surrounding local extrema near the channel location. Monotonicity from the peak is enforced to prevent channels bleeding into each other.

Note

This is likely only applicable for channels inside the brain (intracranial electrodes).

Parameters

montageinstance of mne.channels.DigMontage: The montage object containing the channels.
base_imagestr | pathlib.Path | nibabel.spatialimages.SpatialImage: Path to a volumetric scan (e.g. CT) of the subject. Can be in any format readable by nibabel. Can also be a nibabel image object. Local extrema (max or min) should be nearby montage channel locations.
reg_affinendarray of float, shape (4, 4): The affine that registers one volume to another.
sdr_morphinstance of dipy.align.DiffeomorphicMap: The class that applies the the symmetric diffeomorphic registration (SDR) morph.
subject_fromstr: The name of the subject used for the Freesurfer reconstruction.
subject_tostr: The name of the subject to use as a template to morph to (e.g. ‘fsaverage’).
subjects_dir_fromstr | pathlib.Path | None: The path to the Freesurfer recon-all directory for the subject_from subject. The SUBJECTS_DIR environment variable will be used when None.
subjects_dir_tostr | pathlib.Path | None: The path to the Freesurfer recon-all directory for the subject_to subject. subject_dir_from will be used when None.
threshfloat: The threshold relative to the peak to determine the size of the sensors on the volume.
max_peak_distint: The number of voxels away from the channel location to look in the image. This will depend on the accuracy of the channel locations, the default (one voxel in all directions) will work only with localizations that are that accurate.
voxels_maxint: The maximum number of voxels for each channel.
use_minbool: Whether to hypointensities in the volume as channel locations. Default False uses hyperintensities.
verbosebool | str | int | None: Control verbosity of the logging output. If None, use the default verbosity level. See the logging documentation and mne.verbose() for details. Should only be passed as a keyword argument.

Returns

montage_warpedmne.channels.DigMontage: The modified montage object containing the channels.
image_fromnibabel.spatialimages.SpatialImage: An image in Freesurfer surface RAS space with voxel values corresponding to the index of the channel. The background is 0s and this index starts at 1.
image_tonibabel.spatialimages.SpatialImage: The warped image with voxel values corresponding to the index of the channel. The background is 0s and this index starts at 1.

Examples using `mne.warp_montage_volume`¶

mne.vertex_to_mni

mne.coreg.Coregistration

mne.warp_montage_volume¶

Examples using mne.warp_montage_volume¶

Examples using `mne.warp_montage_volume`¶