Map values to brain subregions in 3D cortex display and generate heat map

wangchenyu · December 11, 2024, 11:05am

Dear experts,

I have data that each brain subregion is associated with a specific percentage value.

Now I need to map these values onto the respective brain subregions of the 3D cortex display to create a heat map, where each subregion is represented by a single color.

In particular, I am seeking methods to map the values to subcortical nuclei (e.g., thalamus and its subregions) and create the heat map.

However, I have not yet discovered how to accomplish this in Brainstorm.

I have also uploaded the data sample here.
sample.mat (38.5 KB)
I need your help.

Thank you!

Wang

Raymundo.Cassani · December 11, 2024, 5:29pm

Hi @wangchenyu, for the moment there is not an option in the GUI to accomplish this, in fact, this feature (3D visualization of scout-space data) is on our roadmap for future features.

However, it is possible to generate this figure with Brainstom, by scripting. The main idea is to create a full source map, and assign the same value to all the vertices in one given scout. To do so the scouts must be the same as in atlas in Brainstorm.

This procedure is shown in the script to generate the Brain fingerprint tutorial. The code is in here:

github.com

brainstorm-tools/brainstorm3/blob/529ea6c29d089a964db353fd4eb9156494ea5816/toolbox/script/tutorial_brain_fingerprint.m#L284-L300


      
          sIccBandMat = db_template('resultsmat');
          sIccBandMat.SurfaceFile = sSurfFile.FileName;
          sIccBandMat.ImageGridAmp = nan(size(sSurfMat.Vertices, 1), 1);
          sIccBandMat.Comment = ['ICC_' BandNames{iBand}];
          sIccBandMat.Time    = [0, 1];
          % Assign ICC values to vertices in Scout
          for ix = 1 : nScouts
              iScout = find(ismember({sAtlas.Scouts.Label}, ScoutNames(ix)));
              sIccBandMat.ImageGridAmp(sAtlas.Scouts(iScout).Vertices) = deal(iccBands(ix, iBand));
          end
          % Output filename
          IccBandFile = bst_process('GetNewFilename', bst_fileparts(sOutputStudy.FileName), 'results');
          IccBandFiles = [IccBandFiles, IccBandFile];
          % Save file
          bst_save(IccBandFile, sIccBandMat, 'v6');
          % Add file to database structure
          db_add_data(iOutputStudy, IccBandFile, sIccBandMat);

wangchenyu · December 12, 2024, 9:50am

Hi

Thank you for your tutorials and I've created the heat map of the cortex.

But I'm still confused about how to generate the heat map for the subregions of thalamus simultaneously.

Looking forward to further guidance from you.
Thanks!

Wang

Raymundo.Cassani · December 12, 2024, 2:27pm

You need to have a Surface with vertices and a surface Atlas with Scouts for those subcortical regions, so you can assign a color to them.

You can obtain this cortex+subcortical surface by merging them, see the first section of this tutorial:

https://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas

After than, you indicated in the post above