Script for right click -> project sources

JonathanC · November 7, 2020, 7:14pm

Hello Francois and other Brainstorm experts,

I'm currently automatizing some steps in my processing pipeline. Some of those steps include things outside the process box. For example, I'd like to automatize a projection of sources on a different surface. When doing it manually, I would right click the source file I want to project and navigate the contextual menus.

My question is where can I find the script that does this step so I could include it in my batch script?

Thank you again for your help,

Francois · November 8, 2020, 9:30am

In general, you can use the Matlab window "Find files" (Ctrl+Shift+F) with the option "Include subfolders", to search for the text of a button or a menu. This will take you to the corresponding callback function.

For example, if you search 'Project sources' (including the quotes), you will find the menu in tree_callbacks.m:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/tree/tree_callbacks.m#L2631


nCortex = nCortex + length(sDefCortex);



% ===== CREATE MENUS =====

% SURFACE: Show a "Project sources" menu if there are more than one cortex avaiable

% or if there is one default cortex and subjects do not use default anatomy

if ismember(HeadModelType, {'unknown','surface','mixed'}) && (nCortex > 1) || ((nCortex == 1) && ~isempty(sDefCortex) && ~UseDefaultAnat)

    if isSeparator

        AddSeparator(jPopup);

    end

    % Project sub-menu

    if (length(ResultFiles) == 1)

        strMenu = 'Project sources';

    else

        strMenu = sprintf('Project sources (%d)', length(ResultFiles));

    end

    jMenu = gui_component('Menu', jPopup, [], strMenu, IconLoader.ICON_RESULTS_LIST, [], []);

    % === DEFAULT ANAT ===

    if ~isempty(sDefCortex)

        jMenuDef = gui_component('Menu', jMenu, [], 'Default anatomy', IconLoader.ICON_SUBJECT, [], []);

        % Loop on all the cortex surfaces

        for iCort = 1:length(sDefCortex)

This will take you to the function bst_project_sources(ResultsFile, DestSurfFile). Then read the header of the function for help. Put a breakpoint in there if you're not sure to understand how it is called from the interface.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/math/bst_project_sources.m

function OutputFiles = bst_project_sources( ResultsFile, destSurfFile, isAbsoluteValues, isInteractive )
% BST_PROJECT_SOURCES: Project source files on a different surface (currents or timefreq).
%
% USAGE:  OutputFiles = bst_project_sources( ResultsFile, DestSurfFile, isAbsoluteValues=0, isInteractive=1 )
% 
% INPUT:
%    - ResultsFile      : Relative path to sources file to reproject
%    - destSurfFile     : Relative path to destination surface file
%    - isAbsoluteValues : If 1, interpolate absolute values of the sources instead of relative values
%    - isInteractive    : If 1, displays questions and dialog boxes
%                         If 0, consider that it is running from the process interface

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2020 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.

This file has been truncated. show original

Francois · November 8, 2020, 9:34am

PS: There is a process "Project on default anatomy" which calls this function to project the source maps on the default surface of the default anatomy, but which won't let you chose which surface you want to use.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/process/functions/process_project_sources.m#L80


    ResultsFile = {sInputs.FileName};
    % Get default anatomy
    sDefSubject = bst_get('Subject', 0);
    if isempty(sDefSubject.iCortex)
        bst_report('Error', sProcess, [], 'No cortex available for the default anatomy.');
        return;
    end
    % Get default cortex of default anatomy
    destSurfFile = sDefSubject.Surface(sDefSubject.iCortex).FileName;
    % Project sources
    switch (HeadModelType)
        case 'surface'
            OutputFiles = bst_project_sources(ResultsFile, destSurfFile, isAbsoluteValues, 0);
        case 'volume'
            OutputFiles = bst_project_grid(ResultsFile, [], 0);
    end
end