fix

Author: Remi-Gau

lib/slice_display

@@ -312,6 +312,7 @@
     end
 
     function results = getResults(obj)
+      %    return results from all nodes
 
       results = struct([]);
       idx = 1;

src/bids_model/BidsModel.m

@@ -1,18 +1,58 @@
 function transparentMontage(opt)
   %
-  % Generate montage with transparent plotting
+  % Generate montage with transparent plotting using slice_display toolbox.
   %
   % USAGE::
   %
   %   transparentMontage(opt)
   %
+  % EXAMPLE::
+  %
+  % opt.pipeline.type = 'stats';
+  %
+  % opt.dir.derivatives = fullfile(this_dir, 'outputs', 'derivatives');
+  % opt.dir.preproc = fullfile(opt.dir.derivatives, 'bidspm-preproc');
+  % opt.model.file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
+  %
+  % opt.subjects = {'01'};
+  %
+  % opt = checkOptions(opt);
+  %
+  % transparentMontage(opt);
   %
 
   % (C) Copyright 2025 bidspm developers
 
-  for i_node = 1:numel(opt.model.bm.Nodes)
+  bm = opt.model.bm;
+
+  modelResults = bm.getResults();
+  if ~isempty(modelResults)
+    opt.results = modelResults;
+  end
 
-    node = opt.model.bm.Nodes{i_node};
+  % loop through the steps to compute for each contrast mentioned for each node
+  for iRes = 1:length(opt.results)
+
+    node = bm.get_nodes('Name',  opt.results(iRes).nodeName);
+
+    if isempty(node)
+
+      id = 'unknownModelNode';
+      msg = sprintf('no Node named %s in model\n %s.', ...
+                    opt.results(iRes).nodeName, ...
+                    opt.model.file);
+      logger('WARNING', msg, 'id', id, 'filename', mfilename(), 'options', opt);
+      continue
+    end
+
+    opt.results(iRes);
+
+    if ~isfield(opt.results(iRes), 'montage') || ~opt.results(iRes).montage.do
+      continue
+    end
+
+    msg = sprintf('\n PROCESSING NODE: %s\n', node.Name);
+    logger('INFO', msg, 'options', opt, 'filename', mfilename());
 
     if any(strcmp(node.Level, {'Run', 'Subject'}))
 
@@ -23,24 +63,15 @@ function transparentMontage(opt)
         ffxDir = getFFXdir(subLabel, opt);
         load(fullfile(ffxDir, 'SPM.mat'));
 
-        for iRes = 1:numel(node.Model.Software.bidspm.Results)
-
-          opt.results = node.Model.Software.bidspm.Results{iRes};
-
-          if ~isfield(opt.results, 'montage') || ~opt.results.montage.do
-            continue
-          end
-
-          % set defaults
-          [opt, ~] = checkMontage(opt, iRes, node, struct([]), subLabel);
-          opt = checkOptions(opt);
-          opt.results(iRes).montage = setMontage(opt.results(iRes));
-
-          for iName = 1:numel(opt.results.name)
+        % set defaults
+        % TODO check plotting is done on the right background
+        [optThisSubject, ~] = checkMontage(opt, iRes, node, struct([]), subLabel);
+        optThisSubject = checkOptions(optThisSubject);
+        optThisSubject.results(iRes).montage = setMontage(optThisSubject.results(iRes));
 
-            plotTransparentMontage(opt, SPM, subLabel, iRes, iName);
+        for iName = 1:numel(optThisSubject.results(iRes).name)
 
-          end
+          plotTransparentMontage(optThisSubject, SPM, subLabel, iRes, iName);
 
         end
 
@@ -53,13 +84,12 @@ function transparentMontage(opt)
 end
 
 function plotTransparentMontage(opt, SPM, subLabel, iRes, iName)
-
+  % Generate a single transparent plot.
+  %
   overwrite = true;
 
   color_map_folder = fullfile(returnRootDir(), 'lib', 'brain_colours', 'mat_maps');
 
-  ffxDir = getFFXdir(subLabel, opt);
-
   if opt.results(iRes).binary
     layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
   else
@@ -80,14 +110,15 @@ function plotTransparentMontage(opt, SPM, subLabel, iRes, iName)
   % - contrast estimates color-coded;
   layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
 
-  name = opt.results.name{iName};
+  name = opt.results(iRes).name{iName};
   tmp = struct('name', name);
   contrastNb = getContrastNb(tmp, opt, SPM);
   % keep track if this is a t test or F test
   stat = SPM.xCon(contrastNb).STAT;
   contrastNb = sprintf('%04.0f', contrastNb);
 
   % - statistics opacity-coded
+  ffxDir = getFFXdir(subLabel, opt);
   if strcmp(stat, 'T')
     colorFile = spm_select('FPList', ffxDir, ['^con_' contrastNb '.nii$']);
     opacityFile = spm_select('FPList', ffxDir, ['^spmT_' contrastNb '.nii$']);
@@ -96,6 +127,7 @@ function plotTransparentMontage(opt, SPM, subLabel, iRes, iName)
 
     load(fullfile(color_map_folder, 'diverging_bwr_iso.mat')); %#ok<*LOAD>
     layers(2).color.map = diverging_bwr;
+
   else
     colorFile = spm_select('FPList', ffxDir, ['^ess_' contrastNb '.nii$']);
     opacityFile = spm_select('FPList', ffxDir, ['^spmF_' contrastNb '.nii$']);
@@ -134,6 +166,7 @@ function plotTransparentMontage(opt, SPM, subLabel, iRes, iName)
   settings.fig_specs.title = title;
 
   %% Display the layers
+  settings.slice.zmm;
   [~, ~, h_figure] = sd_display(layers, settings);
 
   outputFile = fullfile(ffxDir, [contrastNb '_'  name '.png']);