NITRC Surf Ice Forum: help

RE: Is it possible to adjust the smooth parameters?

Chris Rorden — Tue, 28 May 2024 12:39:44 GMT

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.

RE: Is it possible to adjust the smooth parameters?

Victor Altmayer — Mon, 27 May 2024 8:53:48 GMT

Hello <a href="../users/amazinger/">Guochun Yang</a>,  I am facing the same problem, did you find a solution to dicrease the smoothing in SurfIce please ? Best,
Victor

Show activation bar for conjunction map

johezz — Thu, 04 Apr 2024 19:46:56 GMT

Hi Chris!
I have two activation maps that I have read into surfice. As you can see at the top, there are two bars corresponding to each activation map, one for red and one for blue. Is there a way to show the activation bar for the concurrently activated regions (e.g. PURPLE region)?
 
Thank you!
 
Best,
Jo

RE: Increase depth of signal taken into account for cortical projection

Chris Rorden — Tue, 26 Mar 2024 14:57:11 GMT

It is ideal to use Surfice for statistical overlays that are calculated based on mesh vertices rather than voxel intensities. For voxels, you need to project the voxel location onto the mesh, and this will not be accurate, in particular for dilated meshes. Since the voxel to mesh projection is only for illustrative purposes, the implementation is pretty crude. It will either be based on the voxel nearest the vertex (nearest neighbor), or it will compute the average (trilinear interpolation) of the eight voxels nearest the vertex. The choice between these is controlled by "Smooth voxel-based images" in the preferences window. The code is open source, so you can always implement more sophisticated methods. Alternatively, you could convert the voxels to mesh vertices using another tool that saves data in a fomrat Surfice supports, like GIFTI.

Increase depth of signal taken into account for cortical projection

emicroglie — Tue, 26 Mar 2024 13:46:43 GMT

Hello !
I recently realised that what we see in Surf Ice is the intersection between the brain mesh and the 3D file that we display on it, which implies that if a signal is really close to the surface, it won't appear on the smoothest brain meshs. Is there a way to increase the depth of that intersection, so that it would appear anyway (but just less intense, as it would be a mean with voxels containing no signal) ?
 
Thank you in advance !

Regarding csv to rendering on the brain

saimasharleen — Wed, 22 Nov 2023 9:34:47 GMT

Hello, 
I have starting and ending points as two different csv file. How can I render those tracks on the brain?

RE: Visualising subcortical regions (e.g. amygdala)

Chris Rorden — Wed, 15 Nov 2023 15:49:15 GMT

Try Scripting/Templates/Subcortical for various strategies you can use.

Visualising subcortical regions (e.g. amygdala)

johezz — Wed, 15 Nov 2023 15:12:17 GMT

Hello Chris,
 
Thanks for maintaining this forum. I'm wondering how I can visualise subcortical activations, specifically the amygdala, in Surf Ice?
 
Thank you!
 
Best,
Jo

RE: Creating custom atlas meshes

Chris Rorden — Wed, 01 Nov 2023 14:36:46 GMT

https://github.com/neurolabusc/surfice_atlas

Creating custom atlas meshes

Sam Knight — Wed, 01 Nov 2023 11:45:55 GMT

Surfice is such a fantastic tool, the visualisations are beautiful!
I've been trying to create custom mesh atlases from volumetric atlas files. I know there is a function that converts voxelwise meshes to atlases within the application, though I've been having issues getting this to work ('image does not appear to be an atlas' - tried this with my own atlas as well as several more 'standard' ones I've downloaded, same issue).
My hack-job approach was to export each ROI from the .nii and then convert them to .objs, which was successful but I can only add them in individually as overlays and was hoping to create a single file like the standard atlases included.
Do you have any advice for how to create a single .mz3 atlas file?
I've tried following previous threads and using the 'nii_nii2atlas' matlab tool, but I also encounter issues here (same issue with a couple of atlases): 
Converting 122 regions of interest Error using fileUtils.mz3.writeMz3 Too many input arguments.
Error in nii_nii2atlas>img2meshSub (line 109) fileUtils.mz3.writeMz3(outnm, FV.faces, FV.vertices, [], [], false);
Error in nii_nii2atlas (line 51)         img2meshSub(hdrS, imgI, outnm, reduce, thresh, isReverseFace)