1) Bring up mrGray. Load in your project, segment your white matter as usual and make sure that the topology analysis tells you that you have no handles.
2) Now grow gray matter onto the white. Grow exactly 3 layers of gray matter, no more, no less. Save out the gray matter somewhere.
Now build a 3D visualisation. In the 3D visualisation tab box you want to make the following settings...
mrGray will automatically use the current gray file.
Make a note of the voxel dimensions here - you will need to feed them into mrMeshUnfold later.
The other tabs should look like this.....
... and finally....
This final option tells mrGray where to save the mesh file. Make sure you save it somewhere sensible and use the .MrM format.
Now go ahead and build the mesh. The .MrM file should automatically get saved out and you'll be presented with a 3D view of the brain.
Finally, you can pick a start point for the unfold. Position the red, green and blue lines on the 3D volume
and make a note of the X,Y and Z values listed in the toolbar.
and be careful! Note that they're listed in reverse order here (Z,Y,X).
You can also get these valuse by moving around in the 2D segmentation editing window.