Export scout in a nifti file

Luca_Fornia · November 6, 2017, 12:17pm

Dear guys,
I’m looking for export manually draw scout in nifti format in order to be applied as a ROI
for further anatomically analysis, such as a ROI for tractography.
Could you help me,
All the best
Luca

Francois · November 7, 2017, 10:02am

Hi Luca,

The easier is to use volume scouts, then to use the menu Scout > Export as MRI mask (from the Scout tab):
http://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_scouts

If you want to export surface scouts as 3D masks, we do not have any reliable code and therefore no direct export menu. You can maybe assemble something from the function corresponding to the old menu “Edit in MRI” and the “Export as MRI mask” menu:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/gui/panel_scout.m#L4795


                end

                % === SET COLOR ===

                if ScoutsOptions.displayRegionColor

                    scoutColor = GetRegionColor(sScout.Region);

                else

                    scoutColor = sScout.Color;

                end

                set([hScout, hVertices], 'MarkerFaceColor', scoutColor, 'MarkerEdgeColor', scoutColor);

                set(hPatch,   'FaceVertexCData', scoutColor, 'FaceColor', scoutColor);

                set(hContour, 'Color', scoutColor);

            end

        end

        % Redraw completely the missing scouts

        if ~isempty(iScoutPlot)

            PlotScouts(unique(iScoutPlot));

        end

    end

end

drawnow;

if isProgress

    bst_progress('stop');

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/gui/panel_scout.m#L3902


end

% Remove handles

for i = 1:length(sScouts)

    sScouts(i).Handles = sTemplate.Handles;

end

% Save new scout

iNewScout = SetScouts([], 'Add', sScouts);

% Display new scout

PlotScouts(iNewScout);

% Update "Scouts Manager" panel

UpdateScoutsList();   

% Select last scout in list (new scout)

SetSelectedScouts(iNewScout);

end





%% ===== PROJECT SCOUTS =====

function ProjectScouts(srcSurfFile, destSurfFile)

% Get current atlas

[sAtlas, iAtlas, sSurf, iSurf] = GetAtlas();

% Get selected scouts

Cheers,
Francois

reallucas · May 27, 2022, 4:49am

Hi Francois

I have exactly the same request as Luca. However, it seems that your solution has been inapplicable in the current version of the Brainstorm.

Could you please tell me the up-to-date solution to extract manually draw scout in nifti format?

Many thanks,
Yuhan

Francois · May 30, 2022, 7:50am

The solution proposed in this thread works:

Create a volume scout: Tutorials/TutVolSource - Brainstorm
In the Scout tab, menu Scout > Export as MRI mask.