MRI Processing#

Step by step instructions for using gui.coregistration():

coreg.get_mni_fiducials(subject[, ...])

Estimate fiducials for a subject.

coreg.estimate_head_mri_t(subject[, ...])

Estimate the head->mri transform from fsaverage fiducials.

io.read_fiducials(fname[, verbose])

Read fiducials from a fiff file.

io.write_fiducials(fname, pts[, ...])

Write fiducials to a fiff file.

get_montage_volume_labels(montage, subject)

Get regions of interest near channels from a Freesurfer parcellation.

gui.coregistration([tabbed, split, width, ...])

Coregister an MRI with a subject's head shape.

gui.locate_ieeg(info, trans, aligned_ct[, ...])

Locate intracranial electrode contacts.

create_default_subject([fs_home, update, ...])

Create an average brain subject for subjects without structural MRI.

head_to_mni(pos, subject, mri_head_t[, ...])

Convert pos from head coordinate system to MNI ones.

head_to_mri(pos, subject, mri_head_t[, ...])

Convert pos from head coordinate system to MRI ones.


Read a Freesurfer-formatted LUT.

read_lta(fname[, verbose])

Read a Freesurfer linear transform array file.

read_talxfm(subject[, subjects_dir, verbose])

Compute MRI-to-MNI transform from FreeSurfer talairach.xfm file.

scale_mri(subject_from, subject_to, scale[, ...])

Create a scaled copy of an MRI subject.

scale_bem(subject_to, bem_name[, ...])

Scale a bem file.

scale_labels(subject_to[, pattern, ...])

Scale labels to match a brain that was previously created by scaling.

scale_source_space(subject_to, src_name[, ...])

Scale a source space for an mri created with scale_mri().

transforms.apply_volume_registration(moving, ...)

Apply volume registration.


Align two volumes using an affine and, optionally, SDR.

vertex_to_mni(vertices, hemis, subject[, ...])

Convert the array of vertices for a hemisphere to MNI coordinates.

warp_montage_volume(montage, base_image, ...)

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

coreg.Coregistration(info, subject[, ...])

Class for MRI<->head coregistration.