Source Space Plotting

srd2365 · May 23, 2017, 5:11pm

Hi All,

so as part of my analyses, I use a LCMV beamformer to project my EEG data from sensor space to source space. Based on my head model I have 15765 points in source space. I then perform a whole brain searchlight MVPA procedure obtaining a classification accuracy for each searchlight and thus each point in source space. I want to plot the results in a manner similar to the following or generally on an actual Brain Volume/Surface:

Is there a way to do this in brainstorm? Thank you!

Sri

Francois · May 24, 2017, 7:01am

Hello,

If you used a volume head model (no location constraint), you can create a 3D scout around your area of interest and display it on a 3D view of the MRI (you can make them opaque for a more similar view):
http://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_scouts

Otherwise, you can export you source maps as a .nii volume (process: File > Export to SPM8 (volume)) then display this volume the way you want in an external program.

Francois

srd2365 · May 24, 2017, 4:07pm

Thanks Francois,

Thank you for the quick response! To clarify though I know the classification accuracy at each of the 15765 source points. In response to a previous question of mine you said that “These values [at each source point] are reinterpolated over a much denser grid of values to display it in the MRI viewer and overlay it with the subject’s MRI” (Problem exporting volume data).
I was wondering how this reinterpolation is done and if there is anyway I can do it with user specified values (in this case accuracies).

Thanks,

Sri

Francois · May 26, 2017, 7:54am

Here is the function that does this reinterpolation (but it would be difficult to use without the interface):

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/anatomy/grid_interp_mri.m

function grid2mri_interp = grid_interp_mri(GridLoc, MRI, SurfaceFile, isWait, nDownsample, DistanceThresh, GridSmooth)
% GRID_INTERP_MRI: Interpolate a grid of points into a MRI.
%
% USAGE:  grid2mri_interp = grid_interp_mri(GridLoc, MRI, SurfaceFile=[], isWait=1, nDownsample=3, DistanceThresh=2, GridSmooth=1)
%
% INPUT: 
%     - GridLoc        : [Nx3] matrix, 3D positions of the volume grid points
%     - MRI            : Brainstorm MRI structure
%     - SurfaceFile    : Surface to use for the interpolation
%     - isWait         : If 1, show a progress bar
%     - nDownsample    : Volume downsampling factor
%     - DistanceThresh : Maximum distance between a colored voxel and a grid point (in mm)
%     - GridSmooth     : If 1, performs a distance-weighted interpolation with 3 nearest neighbors
%                        If 0, performs a nearest neighbor lookup instead
% OUTPUT:
%     - grid2mri_interp : Sparse matrix [nVoxels, nGridLoc]

% @=============================================================================
% This function is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm

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It could be easier for you simply look into the Matlab interpolation functions (interp3, griddata…)

srd2365 · May 27, 2017, 8:08pm

Thanks Francois! I think I figured out how to use this function and with some other modified code to create the kind of figures I want.