BrainVoyager QX v2.8
Preparing a Mesh for CBA
The first step of the cortex-based alignment procedure is the creation of spherical mesh representations from folded cortex meshes. The input to this morphing stage is the reconstructed cortex of a properly segmented brain hemisphere (i.e. files with names "<subj>_TAL_<LH | RH>_RECOSM.srf". Note that the cortical hemispheres must be without topological errors (e.g. "bridges"), otherwise the morphing and subsequent alignment will fail.
![](Images/CreateMeshExtendedNbrsDlg1.png)
The folded cortex mesh used as input ("LH_RECOSM" or "RH_RECOSM") is the result of a cortex reconstruction ("RECO") from a segmented brain after application of 150 smoothing iterations. Since BrainVoyager QX 1.9 meshes can be reconstructed having more vertex neighbors. These meshes can also be simplified to a mesh with almost the same geometry but with less vertices. When using these meshes, the to-sphere morphing is faster and more robust than when using the standard meshes. More specifically, the following procedure is suggested:
- Reconstruct the mesh (left or right hemisphere) from a segmented volume hemisphere using the Use extended set of neighbors option in the Create Mesh dialog (see snapshot above) and save it as "<name>_RECOx_LH.srf" or "<name>_RECOx_RH.srf" for the left or right hemisphere, respectively. The "x" in the name is used to indicate that a mesh with an extended neighborhood is used.
- Perform 50 (instead of 150 for standard meshes) smooth iterations and save the mesh as "_RECOSMx".
- Simplify the mesh to 80,000 vertices using the "Mesh Simplification" dialog; the default settings in the dialog can be kept (see snapshot below).
![](Images/MeshSimplificationForCBADlg1.png)
The resulting mesh looks the same as the original one. In order to see the changes, switch to wireframe mode. The resulting mesh is automatically stored with a name based on the original name but with a substring indicating the amount of vertices in the simplified mesh. In the example above, the substring "_D80k" is added to the name indicating that the resulting mesh has 80,000 vertices.
While not strictly necessary, it is recommended to compute and overlay a curvature map on the folded cortex mesh since it allows to identify sulci and gyri when the mesh is morphed to a sphere in the succeeding step. In order to overlay a curvature map, enter the Cortex-Based Alignment dialog and click the Curvature button and then the Smoothbutton in the Curvature tab. The snapshot below shows the computed curvature map superimposed on a left hemisphere mesh prepared as described above. The overlaid gradual curvature information (blue -> shades of concave curvature, gold-> shades of convex curvature) roughly indicate sulci (blue) and gyri (gold).
![](Images/CBA1.png)
The mesh is now prepared for the next step - the gradual transformation of the folded mesh into a spherical representation.
Copyright © 2014 Rainer Goebel. All rights reserved.