BrainVoyager QX v2.8

Morphing a Reconstructed Cortex Hemisphere to a Sphere

The next step after preparing a cortex mesh consists in morphing it to a sphere since the CBA algorithm works on spherical representations as a common space with all cortex meshes superimposed that are supposed to be aligned. The to-sphere morphing step is performed separately for the cortex mesh of the left and right hemisphere of each included brain. After loading the prepared hemisphere mesh for a subject, click theMorph button in the 1. Morph mesh to sphere field of the Make Sphere tab of the Cortex-Based Alignment dialog. This will start an iterative morphing process that uses several forces with values that will be changed gradually over time. A smoothing force is used to remove the gyri and sulci from the mesh, while a to-sphere force attempts to push the mesh vertices outward towards points on a sphere. These forces must be coordinated in order to get the desired result without any folding and in a reasonable amount of time. The default number of morphing steps is 800, which will produce a sphere without folding if the default To sphere force and Unfolding correction force values are used. These values should be fine in almost all cases, but you can change them if you experience problems or want to try to further optimize them for your data.

The snapshot above shows the state of the to-sphere morphing process after 126 iteration for a left hemisphere cortex mesh ("RG_RECOSMx_LH_D80k.srf"). At this early stage, the smoothing force is working stronger than the to-sphere force in order to reduce the folding of the mesh. Note that the superimposed curvature information indicates the original folding pattern.

The snapshot above shows the morphing process roughly after half of the morphing has been completed. At this stage the to-sphere force is getting stronger, which is apparent by a rounded shape of the mesh.

When the to-sphere morphing has been completed, the folded cortex mesh has been transformed in a spherical representation. There are, however, some parts, which are expanded - especially mid-lateral and mid-medial parts - and other parts, which are squeezed - especially frontal and occipital regions. In order to correct these distortions as much as possible, a second morphing step must be performed, which is started by clicking the Correct button in the 2. Distortion correction field. The amount of the current mean distortion is depicted in the status bar during morphing. The mean distortion value is obtained by averaging distortion values calculated for each vertex by comparing the current distance of a vertex to its neighbors with the distance values when the mesh was in the original folded state. You will observe that the displayed mean linear distortion value will decline most of the time but it will sometimes also jump to higher values because the distortion correction process uses a "push-relax" approach. The NrOfSteps value is set to a value of 3000, which is normally sufficient to reduce distortions until a plateau is reached where no substantial progress is possible. The value set in the to field of the Distortion correction force is set to a value, which guarantees in most cases that the process will run successfully; if this force is set to a too large value, the mesh might "explode" since neighboring vertices are then pushed too fast leading to folds in the mesh.

The snapshot above shows the distortion correction morphing step after about 1/3 of the overall steps; when comparing this with the sphere in the previous snapshot, it is already visible that the expanded mid-lateral part (around the sylvian fissure) has been corrected substantially by shrinking it.

The snapshot above shows the final state after the distortion correction morphing step has been completed indicating that distortions have been reduced to a minimum. The program automatically presents a Save As dialog with a suggested name to store the resulting sphere mesh; the suggested name uses the original name but adds the "_SPHERE" substring (in the example: "RG_RECOSMx_LH_D80k_SPHERE.srf") allowing to easily identify from the file name that it contains a sphere as a result of morphing the original folded cortex mesh.

After creation of the spherical representation, the created sphere will be sampled from a standard sphere, which is subsequently used during intersubject alignment.

Copyright © 2014 Rainer Goebel. All rights reserved.