Error in defining volume scout with MNI coordinates

Francois · October 8, 2018, 2:52pm

Hi Maryam,

Sorry for the late reply.
What you do seems correct, and I checked but could not reproduce this error.

I think that the error is coming from the fact that the function that creates the scout is not selecting a point (using MNI coordinates) from the correct grid of points. You should make sure the atlas selected is a volume atlas creating when the same source file was opened.

If you still get this error from time-to-time, it means that the other coordinates (the scouts for which you don’t get errors) are probably wrong too. It should be fixed.
If you’re comfortable with Matlab code, open function panel_scout.m, place a breakpoint line 3126 (click on the left of the line in the margin) and then create a new scout using corrdinates that do not work. Then you can follow what is happening by executing the code step by step (button “step over”). If it doesn’t go in section the volume (isVolumeAtlas=1), there is something wrong.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/gui/panel_scout.m#L3126


        bst_error(['The MNI coordinates are not available for this subject.' 10 'Right-click on the MRI file > Compute MNI transformation.'], 'Create scout', 0);

        return;

    end

else

    return;

end



% Get atlas properties: surface or volume

[isVolumeAtlas, nAtlasGrid] = ParseVolumeAtlas(sAtlas.Name);

% Volume atlas: Get grid of points

if isVolumeAtlas

    % Get current figure

    hFig = bst_figures('GetCurrentFigure', '3D');

    if isempty(hFig) || ~ishandle(hFig)

        return

    end

    % Get ResultsFile and Surface

    ResultsFile = getappdata(hFig, 'ResultsFile');

    if isempty(ResultsFile)

        bst_error('No source file loaded in this figure', 'Create new scout', 0);

        return;

Cheers,
Francois