MRI Processing

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

coreg.get_mni_fiducials(subject[, …])

Estimate fiducials for a subject.

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.fiducials([subject, fid_file, subjects_dir])

Set the fiducials for an MRI subject.

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_freesurfer_lut([fname])

Read a Freesurfer-formatted LUT.

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.

transforms.compute_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.