Get the coordinates of a max value from scouts

lulingxi · December 23, 2017, 2:34am

Hello all,

I have an time-averaged sources map (150 - 200 ms averaged) and some scouts I am interested in, and I want to find the max value in each scout and get its coordinates.

I run the command “Extract - Extract Value” and use the “max” option, and then export the result to files. In that file I can read the max value in each scout, but where can I get the corresponding coordinates of that max value?

Thanks
Lingxi

Francois · January 5, 2018, 3:59pm

Hello,

Computing the scout time series using the "max" option in the processes "Extract scout time series" or "Extract values" cannot work because they don't keep the coordinates of the maximum vertices (and if you had multiple time points, it would select probably a different vertex at each time point).

In the Scout tab, you can select all your scouts use the menu Sources > Maximal value (selected scout). It modifies the existing scouts and keep only the vertex with the highest value. Then right-click on the figure > Get coordinates, and select the point where the scout was created. It will give you the coordinates in MRI, SCS and MNI coordinate systems.

Otherwise, you can do it all manually:

Export the source maps to Matlab (http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Custom_processing) => sSources
Export the scouts to Matlab (from the Scout tab: menu Scouts > Export, http://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#On_the_hard_drive) => s1
Export the cortex surface to Matlab (from the database explorer, right-click on the surface > File > Export to Matlab, http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface) => sSurface
Find the vertices with the highest values within scout s1: [valMax, iMax] = max(sSources.ImageGridAmp(s1.Vertices,1));
Get the SCS coordinates of this vertex: sSurface.Vertices(s1.Vertices(iMax), : )
To convert to different coordinate systems: http://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems

Francois

lulingxi · January 10, 2018, 5:12am

Thanks Francois! It helps a lot.

SvTr · April 30, 2020, 12:19pm

Hello Francois!
I've just done what you suggested in this thread, selecting Sources-Maximal value(selected scout), to get the MNI coordinates for that point. But I haven't realized that this would modify the scout forever. Is there any way to undo this? I would really need to restore the original, complete scout since I've already used it for other analyses.
I would greatly appreciate your help,
SvTr

Francois · May 1, 2020, 7:33am

No, unfortunately there is no way to undo any modification to the database, and the scouts are saved only in one file (the cortex surface), no redundancy where you can find your data back.

Hopefully you have a backup set up to restore the previous stage.
If you don't: all your work is at risk, it's time to set up one urgently.

SvTr · May 2, 2020, 9:28am

Hi Francois,
thanks so much for the quick reply! I might actually have a backup on a hard drive. Will try to find the corresponding file! Thanks!

Vardan · December 20, 2020, 7:57pm

Hello Francois!
Can you tell please how to find, for example, 10 vertices within scout with highest values?
This way - "you can select all your scouts use the menu Sources > Maximal value (selected scout). It modifies the existing scouts and keep only the vertex with the highest value" - works for 1 point. What if I want to find 10 points with highest values?

Francois · December 21, 2020, 8:49am

Then you have to code it by yourself. I previously pointed at all the data structures.
You can find inspiration in panel_scout.m > CreateScoutMax:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/gui/panel_scout.m#L2978


    

    % ===== DISPLAY =====

    UpdatePanel();

    PlotScouts(iScout);

    UpdateScoutsDisplay('current');

    SetSelectedScouts(iScout);

end





%% ===== CREATE SCOUT: MAXIMUM VALUE =====

% Usage:  CreateScoutMax(iScout) : Keep only the maximum value in the selected scout

%         CreateScoutMax()       : Create new scout with the vertex with maximum value at current time

function CreateScoutMax(iScout)

    % Prevent edition of read-only atlas

    if isAtlasReadOnly()

        return;

    end

    % Parse input

    if (nargin < 1)

        isNewScout = 1;

    else