How to open a 3D visualization of a computed source from an EEG from script?

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1

Hi everybody!

I need to know how to open a 3D visualization of my computed source from a EEG. I know how to do it from the brainstorm GUI, but I need to do it from inside matlab in the command window. So I need to know how to do what I do in GUI from a script. Maybe I haven't been clear enough, so following is the print screen from my PC where I did what i need from the brainstorm GUI.

brainstorm.jpg1366×768 194 KB

I would really appreciate your help.
Gilliano.

2

Hi Gilliano,

You have a few examples available in the script brainstorm3/toolbox/script/tutorial_ctf.m
This script reproduces the introduction tutorials (#1 to #8).
Is this what you need?

Cheers,
Francois

3

Hi Francois,

thanks for your response. I looked at the tutorial and it seems that it has what I need. However, when I tried to use the example to do what I need in my code, I get an error. Following is my code:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Script generated by Brainstorm (14-Apr-2015)


brainstorm nogui;
import_data;    


% Input files
sFiles = {...
    'NewSubject/Default/data_block001.mat'};


% Start a new report
bst_report('Start', sFiles);


% Process: Compute noise covariance
sFiles = bst_process('CallProcess', 'process_noisecov', ...
    sFiles, [], ...
    'baseline', [0, 547.9980469], ...
    'target', 1, ...
    'dcoffset', 1, ...
    'method', 1, ...  % Full noise covariance matrix
    'copycond', 0, ...
    'copysubj', 0);


% Process: Compute sources
sFiles = bst_process('CallProcess', 'process_inverse', ...
    sFiles, [], ...
    'comment', '', ...
    'method', 1, ...  % Minimum norm estimates (wMNE)
    'wmne', struct(...
         'NoiseCov', [], ...
         'InverseMethod', 'wmne', ...
         'ChannelTypes', {{}}, ...
         'SNR', 3, ...
         'diagnoise', 0, ...
         'SourceOrient', {{'fixed'}}, ...
         'loose', 0.2, ...
         'depth', 1, ...
         'weightexp', 0.5, ...
         'weightlimit', 10, ...
         'regnoise', 1, ...
         'magreg', 0.1, ...
         'gradreg', 0.1, ...
         'eegreg', 0.1, ...
         'ecogreg', 0.1, ...
         'seegreg', 0.1, ...
         'fMRI', [], ...
         'fMRIthresh', [], ...
         'fMRIoff', 0.1, ...
         'pca', 1), ...
    'sensortypes', 'MEG, MEG MAG, MEG GRAD, EEG', ...
    'output', 1);  % Kernel only: shared


% View on the cortex surface
fn='Subject01/@default_study/results_wMNE_EEG_KERNEL_150417_1733.mat';
hFig1 = script_view_sources(fn, 'cortex');
% Set current time to 46ms
panel_time('SetCurrentTime', 0.046);
% Set surface threshold to 75% of the maximal value
iSurf = 1;
thresh = .75; 
panel_surface('SetDataThreshold', hFig1, iSurf, thresh);
% Set surface smoothing
panel_surface('SetSurfaceSmooth', hFig1, iSurf, .4);
% Show sulci
panel_surface('SetShowSulci', hFig1, iSurf, 1);




% Save and display report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

When I try to run, I get this error message:

What I am doing wrong?

4

Hello,

Your script looks good!
There is just some confusion about the source file that you are trying to display.
Because you have selected the option “output=1” (Kernel only: shared), it creates a shared kernel, then applies it to the recordings available in the same subject or folder. If those notions are not clear, go back to the tutorials:
http://neuroimage.usc.edu/brainstorm/Tutorials/TutSourceEstimation#Computing_sources_for_multiple_data_files

If you have only one recording block in your subject, you do not need a shared kernel, you can select the option “Kernel only: one per file”.
Then, you can also avoid having to enter the source file name (or the link file name), and directly get it from the output of the last process call:
fn = sFiles(1).FileName;

Cheers,
Francois

5

It worked! I’ve changed the output parameter from “1” to “2” (Kernel only: one per file) and it fixed. Thanks for your help!