NITRC Surf Ice Forum: help

RE: remove overlays option

Chris Rorden — Thu, 04 Sep 2025 12:18:21 GMT

Jeremy
This is a core feature of Surfice's successor NiiVue. You can try this out in the NiiVue Desktop release:   https://github.com/niivue/niivue/releases for more details on NiiVue meshes, see the documentation   https://niivue.com/docs/mesh

remove overlays option

Jeremy Purcell — Thu, 04 Sep 2025 3:38:59 GMT

Hi Chris,
Amazing tool! One suggestion though for a future release. It would be useful to be able to remove an overlay from view without removing all of the loaded overlays (not just unselect the check box, but actually remove). This would make the functionality and user interaction more similar to mricrogl. 
Best!
Jeremy

Citation

Chris Rorden — Thu, 24 Jul 2025 13:24:40 GMT

For scientists who use Surfice for their work, I would be grateful if you would consider including a citation in your publications: Rorden C (2025) Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes. Nature Methods. doi: 10.1038/s41592-025-02764-6.    https://www.nature.com/articles/s41592-025-02764-6

RE: Adjusting color for ROI figure

Chris Rorden — Thu, 23 Jan 2025 14:03:36 GMT

I think currently the RGB value is the default color for the atlas. We have added support for allowing each label to have a custom transparency (Alpha) and RGB in NiiVue, and it is on the roadmap to back port these colormaps to Surfice and MRIcroGL
The NiiVue colormaps are described here:
 
https://github.com/niivue/niivue/blob/main/docs/development-notes/colormaps.md
You can try this out in the live demo:
https://niivue.github.io/niivue/features/segment.html
 
Note in the live demo you can paste and apply a custom color table. For example, to make gray matter opaque and the other labels transparent you would set the "A"lpha like this:
 
let cmap = {  R: [0,   0, 120, 175],  G: [0,  90,  60, 185],  B: [0, 120,  60, 175],  A: [0, 0,  255, 0],  labels: ["air","CSF","gray","white"], };

Adjusting color for ROI figure

Tom Willems — Wed, 22 Jan 2025 18:22:58 GMT

Hello
 
I would like to create a figure that illustrates the ROIs that were analysed.
I found an example where the region color is determined by statistical values, but can it be just freely assigned via rgb value?
my example:  import gl gl.resetdefaults() gl.azimuthelevation(240, 15) gl.azimuthelevation(240, 15); gl.meshload('aal.mz3') gl.atlasstatmap('aal.mz3',              'surficetemp.mz3',      (23,24,31,32,37,38,39,40,45,46,85,86,89,90),      (0.5, 0.5, 1,1, 2, 2,3, 3, 4,4,5,5, 10,10)) gl.meshload('BrainMesh_ICBM152.mz3') gl.shaderxray(0.5, 0.5) gl.overlayload('surficetemp.mz3');
 Many thanks in advance Tom

RE: Control color and brightness of individual or groups of nodes

Chris Rorden — Wed, 06 Nov 2024 12:45:05 GMT

Surfice only allosws the user to load one set of connectome nodes at a time. You can use a threshold on the color or intensity to only show some nodes and hide others. The simple solution is to write a Python script to concatenate nodes from multiple files as a single file for each image. It is easy to add support for multiple node files, but providing an intuitive user interface is tricky.
 
The other option is to use NiiVue that allows multiple independent node files. https://niivue.github.io/niivue/features/labels.connectomes.html

Control color and brightness of individual or groups of nodes

Leo Sugrue — Wed, 06 Nov 2024 5:24:27 GMT

Hi there - 
I am trying to use surf ice node feature to display the locations of contacts from SEEG electrodes. I am doing this by treating each contact location as a 'node' and loading a .node file.
However, I really want to be able to a) load the contacts in groups (corresponding to electrodes targeting a given structure) with a different color, and b) ideally load the contacts with color intensities that reflect some behavioral or physiological effect.
So far I can only load one set of nodes at a time and they all have the same color. It seems like there ought to be a way to specific color and intensity for each node individually but I can't seem to figure out how to do it.
Any guidance would be much appreciated.
Leo

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