Flattening

Original

http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/Visualization#Creating_a_Flat_view_from_a_mesh

We use a flattening tool (by Alex Wade) to create a flattened representation from a mesh.This tool is usually invoked from the Volume view of mrVista. In that view, the user selects a point in cortex and a radius for flattening. The mesh is flattened and the data from the Volume view are then projected into a Flat view.

The Flat page contains information on performing analyses on the flat view, including using the 'Atlas' model of retinotopic structure.

The tool is accessible via the Segmentation menu in a Volume or Gray window. The tool begins with a gray/white segmentation data and a mesh, and then flattens cortex within a distance of a starting point. You specify both the starting point and the distance. (This differs from the approach by most BrainVoyager users, who flatten the entire cortex. Each has their advantages.)

To create a Flat window data type, you must have:

• a data session initialized in mrVista (see Functional)
• an anatomical that has been segmented.
• an Alignment to the reference volume
• an open gray or volume window

To flatten, select an ROI which includes gray matter in the hemisphere you would like to flatten, around the center of the disc you would like to use. Select

Gray | Flat Patch | Create flat patch start from center of current ROI.

and mrFlatMesh will start. The window looks like:

mrFlatMesh

* RE-WRITE MATERIAL BELOW FOR ITKGRAY CLASSIFICATION FILES AND INPUT *

Several input fields must be set. The top two file fields show the location of the gray matter graph (*.gray or *.Gray) and the 3D mesh (in mrGray format, *.MrM) for the relevant segmentation. Normally, mrFlatMesh can guess the hemisphere of your ROI, and get the corresponding path, but sometimes you will need to set it. You can press the browse buttons to get a dialog to find the files.

(The .MrM files are generally stored in the 3DMeshes/ subdirectory of a segmentation. If you don't have one, you can create one in mrGray by loading the appropriate mrGray project file, and selecting 3D | Build Visualization. In the dialog this creates, make sure you have the 'save output mesh file' checkbox on.)

You also specify the radius of the disk in mm. Larger radii may take more time to unfold, and may lead to greater area distortions, but allow you to see more of the cortex. I (Rory) have found that going significantly above 100 mm radius can cause even a modern machine to run out of memory, so be careful there.

Also set an informative name for the output unfold file (which will be a matlab .mat file, containing all relevant information on the unfold). Press Go when you're ready. Depending on the size of the unfold and the machine, this can take anywhere from 10 min to 2 hours. The code will provide some feedback in the message log at the bottom of the window, but sometimes it is fairly silent (and so can seem like it is frozen up). It generally chugs through, though; and if it runs out of memory it lets you know at the beginning. (Rory has found, on a 3GHz machine, that a 0mm-raidus disk unfolds in about 25 minutes, and a 90mm-radius disk in about 40 minutes.)

If you leave the 'figures' checkbox selected in mrFlatMesh, the code will produce the following output figures:

Unfolded mesh nodes		Manifold distance map
Flat Level Nodes: Each image shows one 'layer' of flat nodes, starting at the gray/white interface and moving towards the pial surface. The gaps in higher levels occur because in many parts of cortex, the segmentation can't find another node higher up: there's either other gray matter (as in a sulcus) or CSF.		Amount of curvature on the selected mesh. Higher values indicate more curvature, and tend to correspond to gyri, while lower values corespond to sulci.

Once you've created the unfold or unfolds (for both hemispheres), you can attach them to your mrVista sessions. From the Gray menu, select Flat Patch | Install New Unfold. A dialog will prompt for the name of the unfold: since you may want to produce different patches for different parts of cortex, you can have different sorts of flat views. It will then ask for the unfold files (which are .mat files produced by mrFlatMesh) for the left and right hemispheres. You only need to produce an unfold file for one hemisphere, if you haven't segmented or flattened (or imaged) the other one; just select 'cancel' for the hemisphere you don't want to install.

You will then have a Flat view initialized. Use the Flat page for more information on how to use this view.