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aces / brainbrowser

Web-based visualization tools for neurological data.
https://brainbrowser.cbrain.mcgill.ca/
GNU Affero General Public License v3.0
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Two MNI .obj Surfaces in the Same Space #346

Open blahner opened 5 years ago

blahner commented 5 years ago

In BrainBrowser Surface Viewer, I wish to overlay a surface region of brain activation (EVC for example) on the example "brain with cortical thickness map" (The "brain-surface.obj" template), but they are not in the same space or scaled the same. The brain-surface.obj file is an MNI .obj and my brain activation surface is a Wavefront .obj file. How can I convert from Wavefront .obj to MNI .obj and ensure the brain and activation surface are in the same space and scaled correctly? I am able to open the template brain's MNI .obj file and look inside, but I cannot figure out where the spatial and scaling information lies. I appreciate your help!

lblewis commented 5 years ago

I would assume that the provided example "brain with cortical thickness map" is from an individual brain completely unrelated to whatever data it is that you are bringing. The only way that it would be in the same space is if your map were already computationally resampled to that individual (offline from BrainBrowser, which is probably not of interest). If your map is from an individual subject, you need to provide that same individual subject's .obj (regardless of whether MNI or Wavefront). If the map has already been resampled to an average surface template (such as CIVET's ICBM or Freesurfer's fsaverage), then you need to provide that matching surface template. The questions you are asking sound like they are more about surface registration, not about BrainBrowser per se...

blahner commented 5 years ago

Thank you for your help and response. That is all good to know. Like you suggested, I am able to align my activation data with a matching surface template, just not with the "brain with cortical thickness map." I will keep on trying with that, or else I will have to be satisfied with the template I do have. A BrainBrowser question that I do have is about coloring an uploaded surface. I wish to include a heat map on my activation region (specific to my data) but I am unable to upload it in any color. The region appears as all black. I include the color information after each vertex coordinate in the .obj file, and other software (like meshlab) is able to visualize the color, but not brainbrowser. I am also unable to upload the color as a per-vertex text file. Do you have any suggestions? Thanks!

lblewis commented 5 years ago

I don't think BrainBrowser has the function to show colors embedded in the surface file (maybe one of the coding team can correct me if I am wrong). But I would think that uploading a per-vertex text file should have been fine. It should simply be a list with one value per line / vertex. For example, if you had 5 vertices, and 3 colors, it would look something like:

3 1 2 1 2