Leadfield information in bst

abdallahqusaibe · November 20, 2020, 1:47pm

Hello,

I would like to use only normal-oriented sources, so that each vertex position had only one source that was oriented normal to the local cortical surface,

(I know that I can do it in the source estimation to choose the constrained source) but my question how can I have the leadfield with the axis oriented normal to the local cortical surface,
because in Brainstorm the output of the leadfield is Number of sensors X (3 X Number of source), so how can I have leadfield as: Number of sensors X (1 X Number of source (where the orientation is oriented normal to the local cortical surface ))

Thank in advance!

Francois · November 20, 2020, 4:53pm

The leadfield is always computed for 3 orientations at each point.
To apply an orientation constraint to it, use bst_gain_orient.m:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/forward/bst_gain_orient.m

function Gain = bst_gain_orient(Gain, GridOrient, GridAtlas)
% BST_GAIN_ORIENT: Constrain source orientation on a leadfield matrix
%
% USAGE:  Gain = bst_gain_orient(Gain, GridOrient, GridAtlas)
%
% INPUT: 
%     - Gain       : [nChannels,3*nSources] leadfield matrix
%     - GridOrient : [nSources,3] orientation for each source of the Gain matrix
% OUTPUT:
%     - Gain : [nChannels,nSources] leadfield matrix with fixed orientations

% @=============================================================================
% 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

Use the VertNormal list of normals from the cortex surface:
Gain_normal = bst_gain_orient(sHeadModel.Gain, sSurface.VertNormals);

abdallahqusaibe · December 2, 2020, 3:23pm

Hi Francois,

The step that I did,

Computed the head model using cortex surface (source space)
exported the computed gain and cortex_15002V to the matlab
applying what you suggested
Gain_normal = bst_gain_orient(gain.Gain, cortex_15002V.VertNormals);
Then I put this new Gain_normal matrix instead of the previos one (102x45006)

5) then I imported again this new gain, when I view the lead field I get this error:

when I simulate from scout I have also another error:

image1103×451 16.5 KB

can you help me please?

Francois · December 3, 2020, 3:32pm

In the headmodel files saved in the Brainstorm database, the Gain matrix must remain defined for all the orientations.
The field GridOrient in the same file is applied on the fly when reading the head model for estimating the sources:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_bst_headmodel.m#L133


        % Read full gain matrix

        HeadModel.Gain = old_read_gain(gainfile);

    else

        HeadModel.Gain = double(HeadModel.Gain);

    end



    % === APPLY ORIENTATIONS ====

    % If the gain matrix has 3 orientations per source, we need to apply the orientation

    if ApplyOrient && (size(HeadModel.Gain,2) == 3 * length(HeadModel.GridOrient))

        % Apply the fixed orientation to the Gain matrix (normal to the cortex)

        HeadModel.Gain = bst_gain_orient(HeadModel.Gain, HeadModel.GridOrient);

    end

end



%% ===== READ COMMENT =====

if isfield(HeadModel, 'HeadModelName') && ~isfield(HeadModel, 'Comment')

    HeadModel.Comment = HeadModel.HeadModelName;

end



%% ===== READ HEAD MODEL TYPE =====

if isfield(HeadModel, 'HeadModelType')