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+====== NeuroElf - GUI Scripting ======
+===== Motivation =====
+While using the GUI manually (browsing maps, setting thresholds, etc.) is usually the first step in getting a feel for the data, sometimes it is yet convenient to create a set of images (screenshots, etc.) that all have the same properties, which then becomes a matter for scripting.
+NeuroElf thus offers the capability to control much of the behavior available via mouse clicks as function calls to the neuroelf_gui function.
+===== Requirements =====
+In the presented case, a GLM file was manually opened, and a VMP file was pre-created containing the result of regression maps.
+===== Script =====
+<code matlab negui_script_example.m>% get global access to NeuroElf GUI config (ne_gcfg)
+global ne_gcfg;
+% list of maps to cluster and show effects of
+maps = [1, 2, 11, 12, 21, 22, 31, 32];
+% get handle to xff class
+x = xff;
+% which file to use as underlay for display
+try
+    vmr = x('colin_brain_ICBMnorm.vmr');
+catch
+    vmr = neuroelf_file('c', 'colin_brain_ICBMnorm.vmr');
+end
+vmr.Browse;
+% load VMP
+try
+    vmp = x('reappdevel_38subs_agesquared_correl.vmp');
+catch
+    vmp = xff('/Volumes/reappdevel/Imaging/bv_analyses/reappdevel_38subs_agesquared_correl.vmp');
+end
+vmp.Browse;
+% open montage window
+neuroelf_gui('vismontage');
+drawnow;
+% options for montage images
+miopt = struct( ...
+    'atrans',    false, ...
+    'atranscol', [0, 0, 0], ...
+    'blx',       [1, 1], ...
+    'brds',      0, ...
+    'drc',       1, ...
+    'drs',       256, ...
+    'filename',  './X.png', ...
+    'flp',       false, ...
+    'flx',       false, ...
+    'frame',     [128, 128, 128; -127.99, -127.99, -127.9999], ...
+    'hFig',      xfigure('Wnd_NeuroElf_vismontage'), ...
+    'imeth',     'linear', ...
+    'imetha',    'linear', ...
+    'join',      true, ...
+    'ppv',       4, ...
+    'showinfig', false, ...
+    'slvar',     vmr, ...
+    'stalp',     1, ...
+    'stthr',     [0.1, 1.0], ...
+    'stvar',     vmp, ...
+    'stvix',     1, ...
+    'sws',       false, ...
+    'tpvol',     1);
+% get (Matlab UI) handle of all beta plot windows
+cfigs = fieldnames(ne_gcfg.cc);
+bpfig = cfigs(~isemptycell(regexpi(cfigs, '^BP')));
+bpglm = bpfig;
+bpglmf = bpglm;
+bpglmvb = bpglm;
+for fc = 1:numel(bpfig)
+    bpglm{fc} = ne_gcfg.cc.(bpfig{fc}).Config.glm;
+    bpfig{fc} = ne_gcfg.cc.(bpfig{fc}).SatelliteMLH;
+    [glmpath, bpglmf{fc}] = fileparts(bpglm{fc}.FilenameOnDisk);
+end
+bpfig = cat(1, bpfig{:});
+% set figure size(s)
+set(bpfig, 'Position', [100, 100, 1024, 768]);
+% iterate over maps
+for mc = 1:numel(maps)
+    % get map number and name
+    mn = maps(mc);
+    mnm = makelabel(vmp.Map(mn).Name);
+    % enable clustering thresholds and two-tailed test
+    vmp.Map(mn).ClusterSize = 57;
+    vmp.Map(mn).EnableClusterCheck = 1;
+    vmp.Map(mn).ShowPositiveNegativeFlag = 3;
+    % set as current map
+    neuroelf_gui('setcstatmap', mn);
+    % enforce correct threshold
+    neuroelf_gui('setstatthrpval', 0.01);
+    % create cluster table
+    neuroelf_gui('clustertable');
+    % continue if no clusters
+    if isempty(ne_gcfg.voi.VOI)
+        continue;
+    end
+    % set map in options for montage image
+    drawnow;
+    miopt.stvix = mn;
+    miopt.stthr = [vmp.Map(mn).LowerThreshold, vmp.Map(mn).UpperThreshold];
+    % restrict clusters to 8mm spheres
+    neuroelf_gui('setcluster', 'set', 1:numel(ne_gcfg.voi.VOI));
+    neuroelf_gui('limitclusters', {8, 's'});
+    % get VOI object handle
+    voi = ne_gcfg.voi;
+    % extract betas
+    for fc = 1:numel(bpglm)
+        bpglmvb{fc} = bpglm{fc}.VOIBetas(voi);
+    end
+    % iterate over clusters
+    for cc = 2:2:numel(voi.VOI);
+        % get coordinate and text
+        svoi = voi.VOI(cc);
+        svoic = svoi.Voxels(1, :);
+        svoin = regexprep(svoi.Name, '^.*_(.H_.*)$', '$1');
+        svoin = regexprep(svoin, '_sph.*$', '');
+        svoin = regexprep(svoin, '_+$', '');
+        % build cluster name
+        clname = sprintf('%s%s_%d_%d_%d', mnm, svoin, svoic(1), svoic(2), svoic(3));
+        % set cluster
+        neuroelf_gui('setcluster', 'set', cc);
+        % draw and update
+        pause(0.01);
+        drawnow;
+        pause(0.01);
+        % handle barplots
+        for fc = 1:numel(bpfig)
+            % get frame(s) from figure(s)
+            bplot = getframe(bpfig(fc));
+            % save as PNGs
+            imwrite(bplot.cdata, sprintf('%s_%s_plot.png', bpglmf{fc}, clname));
+            % save extract data as well
+            vb = bpglmvb{fc}(:, [2, 4, 6], cc);
+            save(sprintf('%s_%s_extract.txt', bpglmf{fc}, clname), 'vb', '-ascii');
+        end
+        % create three panel views
+        miopt.drc = 1; % SAG
+        miopt.filename = sprintf('%s_%s_SAG.png', bpglmf{fc}, clname);
+        miopt.frame = [128, 128, 128; svoic(1), -127.99, -127.9999];
+        neuroelf_gui('vismontage_create_ex', miopt);
+        miopt.drc = 2; % COR
+        miopt.filename = sprintf('%s_%s_COR.png', bpglmf{fc}, clname);
+        miopt.frame = [128, 128, 128; -127.99, svoic(2), -127.9999];
+        neuroelf_gui('vismontage_create_ex', miopt);
+        miopt.drc = 3; % TRA
+        miopt.filename = sprintf('%s_%s_TRA.png', bpglmf{fc}, clname);
+        miopt.frame = [128, 128, 128; -127.99, -127.99, svoic(3)];
+        neuroelf_gui('vismontage_create_ex', miopt);
+    end
+end</code>
+===== Remarks =====
+Many aspects of this script can still be adapted, such as the settings for the single-slice montage images, or the thresholding options. The usefulness of such a script is, of course, questionable, and without a doubt a more sophisticated script (e.g. one that re-loads images and combines them to a panel, etc.) could be devised. However, it is important to understand that this is meant as a starting point!

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