Dear experts,

Thanks a lot for the wonderful visualization software.

I am wondering if it is possible to adjust (decrease) the smoothing parameters (e.g., FWHM) of the voxels, because the current smoothing makes some of my brain clusters connected like they are from one cluster while I want to show they are isolated. I am also not satisfied with the output without smoothing. So it would be perfect if I can adjust the smoothing FWHM value. You may see the comparison between smoothed and unsmoothed results in the attached figure.

Thanks!

Guochun

Trying to map voxels onto a mesh surface will always be tricky. In particular, when you want to map voxels form a scan normalized to MNI space to a very inflated mesh: in this case there is not a one-to-one correspondence. I think the blurring helps reflect the ambiguity of the transform. For accurate mapping you will want to conduct the statistics directly on the vertices, you can use tools like FreeSurfer or PALM that will help you with. In this case, each individual's brain is warped to an inflated mesh and the statistics are run in this space. Surfice is a visualization tool, not a statistics tool, so these operations are handled by different tools.

Thanks for your reply.

I apologize for not having described my question very clearly. The "smoothed" I mentioned refers to the option of SurfIce (Help->Preferences->Smooth Voxel-based images). The two panels in my previously posted figure were based on the same nifti file, but with the "Smooth Voxel-based images" option checked and unchecked, respectively. I was asking if the parameters of such "Smooth" built in Surfice can be adjusted. I do want to use Surfice as visualization  purpose only.

Hope this is clearer and look forward to your further help.

Thanks!

Understood. That command in Surfice is very primitive, and is only designed to give an approximation. I am not planning on making that algorithm more sophisticated as I think the number of parameters that could be tuned is huge and beyond the scope of a visualization tool. Surfice is open source, so you can always tune the code for your needs.
If you prefer Matlab, you can use the MRIcroS code:
https://github.com/bonilhamusclab/MRIcro...

Thank you very much!

Hello Guochun Yang, 

I am facing the same problem, did you find a solution to dicrease the smoothing in SurfIce please ?

Best,

Victor

There is not perfect solution for interpolating voxel intensity to mesh vertices. One could argue for maximum intensity within a search radius, nearest neighbor, trilinear interpolation, etc. Surfice is a visualization tool, and the per-vertex colors make the most sense for statistical calculations estimated per-vertex not per-voxel. I see this issue as out of scope for a visualization tool. Feel free to write your own Python tool using nibabel to provide your own preferred solution for this problem.