Visualising ROIs

[neurotix93]

Hi, thanks for this great tool. A quick one - it seems the default visualisation for ROIs is surface based in gmsh, which sometimes makes them look incomplete or unusual.

I believe this is maybe a visualisation error? Rather than an error with the ROI extraction itself.

[idossha]

Hi Laith,

There is no issue/bug here. But two possible explanations:

1. See attached screenshot. Please make sure in Gmsh that under Tools/Visibility you have both surfaces and volumes selected. Then make sure to click apply. I suspect you have only surfaces visible.

2. If above point does not work (though it should), try to run the optimization with both GM and WM enabled. Then repeat the process above. It could be that your subject segmentation has mostly WM in the ROI. Though if you ran into that issue with all your subjects, I feel even better that point 1 should fix it.

If it does, I can look to change the default visualization to have volume enabled. I believe it is only surface by default because it simply renders the model faster, plus most users use Freeview in voxel space when dealing with sub-cortical targets.

Best,
Ido