Warping the anatomy templates

Authors: Francois Tadel, John C Mosher

The best results for source localization are obtained with an individual anatomy of each subject, that are processed to extract the cortex and the scalp surface. Unfortunately, scanning a subject in an MRI costs in time and money, and may not be available for the source analysis. You can use a template anatomy (ICBM152, Colin27 or other), but for subjects with head shapes that are very different from the template the localization errors can be large.

For this purpose, Brainstorms offers an intermediate solution: Creating a pseudo-individual anatomy based on the head points that were digitized before the MEG/EEG acquisition. These points really represent the shape of the head of the subject, they can be used to scale and deform the template MRI and surfaces.

Prepare the anatomy template

The anatomical landmarks (NAS, LPA, RPA) defined when digitizing the head shape must be the same as the ones used in the default anatomy of the protocol (Colin27, ICBM152, FSAverage). By default, the LPA/RPA points are defined at the junction between the tragus and the helix, as represented with the red dot in the Coordinates systems page.

If you want to use an anatomy template but used a different convention when digitizing the position of these points, you have to modify the default positions of the template with the MRI Viewer.

Prepare the subject

We are going to test this feature with the protocol TutorialIntroduction (from the introduction tutorials).

Edit the initial MRI/MEG registration

The warping process is very sensitive to the initial position of the head points relatively to the scalp surface. You really want to make sure that the alignment is correct before running the deformation of the default anatomy, and fix it if necessary. We do not recommend to use the automatic registration at this point, because we are trying to align these points on a completely different head shape. We are going to edit the registration manually.

Warping the template anatomy


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Tutorials/TutWarping (last edited 2016-08-02 20:58:13 by FrancoisTadel)