From cc07d9519c9f8ec0ec05a9199a0f0788a0e360c2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 25 Feb 2025 17:00:01 +0100
Subject: [PATCH 01/12] tmp

---
 demos/MoAE/moae_03_slice_display.m | 30 ++++++++----------------------
 1 file changed, 8 insertions(+), 22 deletions(-)

diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index e08c7a46..8ab8bdd5 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -31,18 +31,10 @@
 
 opt.model.file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
 
-% Specify the result to compute
-opt.results(1).nodeName = 'run_level';
-
-opt.results(1).name = 'listening';
-% MONTAGE FIGURE OPTIONS
-opt.results(1).montage.do = true();
-opt.results(1).montage.slices = -4:2:16; % in mm
-% axial is default 'sagittal', 'coronal'
-opt.results(1).montage.orientation = 'axial';
-% will use the MNI T1 template by default but the underlay image can be changed.
-opt.results(1).montage.background = ...
-    fullfile(spm('dir'), 'canonical', 'avg152T1.nii');
+% read the model
+opt = checkOptions(opt);
+
+opt.results = opt.model.bm.Nodes{1}.Model.Software.bidspm.Results{1};
 
 opt = checkOptions(opt);
 
@@ -55,10 +47,6 @@
 
 rightRoiFile = bids.query(BIDS_ROI, 'data', filter);
 
-filter.hemi = 'L';
-
-leftRoiFile = bids.query(BIDS_ROI, 'data', filter);
-
 % we get the con image to extract data
 ffxDir = getFFXdir(subLabel, opt);
 maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
@@ -66,7 +54,7 @@
 conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
 
 %% Layers to put on the figure
-layers = sd_config_layers('init', {'truecolor', 'dual', 'contour', 'contour'});
+layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
 
 % Layer 1: Anatomical map
 [anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel);
@@ -100,20 +88,18 @@
 
 %% Layer 3 and 4: Contour of ROI
 
+roi = spm_select('FPList', ffxDir, ['^sub_.*' bf.entities.label '.*_mask.nii$']);
+
 layers(3).color.file = rightRoiFile{1};
 layers(3).color.map = [0 0 0];
 layers(3).color.line_width = 2;
 
-layers(4).color.file = leftRoiFile{1};
-layers(4).color.map = [1 1 1];
-layers(4).color.line_width = 2;
-
 %% Settings
 settings = sd_config_settings('init');
 
 % we reuse the details for the SPM montage
+settings.slice.disp_slices = opt.results(1).montage.slices;
 settings.slice.orientation = opt.results(1).montage.orientation;
-settings.slice.disp_slices = -15:3:18;
 settings.fig_specs.n.slice_column = 4;
 settings.fig_specs.title = opt.results(1).name;
 

From 4b25c7fced52777d79bcd5da232d0a94369344e3 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 5 Mar 2025 12:08:01 +0100
Subject: [PATCH 02/12] [DATALAD] Recorded changes

---
 demos/MoAE/moae_03_slice_display.m | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index 8ab8bdd5..b39e5d8d 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -38,15 +38,6 @@
 
 opt = checkOptions(opt);
 
-use_schema = false;
-BIDS_ROI = bids.layout(opt.dir.roi, 'use_schema', use_schema);
-
-filter = struct('sub', subLabel, ...
-                'hemi', 'R', ...
-                'desc', 'auditoryCortex');
-
-rightRoiFile = bids.query(BIDS_ROI, 'data', filter);
-
 % we get the con image to extract data
 ffxDir = getFFXdir(subLabel, opt);
 maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
@@ -60,7 +51,6 @@
 [anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel);
 layers(1).color.file = anat_normalized_file;
 layers(1).color.range = [0 anatRange(2)];
-
 layers(1).color.map = gray(256);
 
 %% Layer 2: Dual-coded layer
@@ -83,14 +73,12 @@
 spmTImage = spm_select('FPList', ffxDir, ['^spmT_' bf.entities.label '.nii$']);
 layers(2).opacity.file = spmTImage;
 
-layers(2).opacity.range = [2 3];
+layers(2).opacity.range = [0 3];
 layers(2).opacity.label = '| t |';
 
 %% Layer 3 and 4: Contour of ROI
-
-roi = spm_select('FPList', ffxDir, ['^sub_.*' bf.entities.label '.*_mask.nii$']);
-
-layers(3).color.file = rightRoiFile{1};
+contour = spm_select('FPList', ffxDir, ['^sub.*' bf.entities.label '.*_mask.nii']);
+layers(3).color.file = contour;
 layers(3).color.map = [0 0 0];
 layers(3).color.line_width = 2;
 

From 32aa8ef9d7eaa57eacdc5625c8514aa2e4b05344 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 5 Mar 2025 14:25:33 +0100
Subject: [PATCH 03/12] refactor

---
 demos/MoAE/moae_03_slice_display.m       | 21 +++++--
 demos/MoAE/return_normalized_anat_file.m | 26 ---------
 src/stats/results/checkMontage.m         | 70 ++++++++++++++++++++++++
 src/workflows/stats/bidsResults.m        | 59 --------------------
 4 files changed, 87 insertions(+), 89 deletions(-)
 delete mode 100644 demos/MoAE/return_normalized_anat_file.m
 create mode 100644 src/stats/results/checkMontage.m

diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index b39e5d8d..72b5bc48 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -31,15 +31,25 @@
 
 opt.model.file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
 
+opt.subjects = [subLabel];
+
 % read the model
 opt = checkOptions(opt);
 
-opt.results = opt.model.bm.Nodes{1}.Model.Software.bidspm.Results{1};
+iRes = 1;
+
+opt.results = opt.model.bm.Nodes{iRes}.Model.Software.bidspm.Results{1};
+
+node = opt.model.bm.Nodes{iRes};
+[opt, BIDS] = checkMontage(opt, iRes, node, struct([]), subLabel);
 
 opt = checkOptions(opt);
 
+opt.results(iRes).montage = setMontage(opt.results(iRes));
+
 % we get the con image to extract data
 ffxDir = getFFXdir(subLabel, opt);
+
 maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
 bf = bids.File(spm_file(maskImage, 'filename'));
 conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
@@ -48,9 +58,12 @@
 layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
 
 % Layer 1: Anatomical map
-[anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel);
-layers(1).color.file = anat_normalized_file;
-layers(1).color.range = [0 anatRange(2)];
+layers(1).color.file = opt.results(iRes).montage.background{1};
+
+hdr = spm_vol(layers(1).color.file);
+[max_val, min_val] = slover('volmaxmin', hdr);
+layers(1).color.range = [0 max_val];
+
 layers(1).color.map = gray(256);
 
 %% Layer 2: Dual-coded layer
diff --git a/demos/MoAE/return_normalized_anat_file.m b/demos/MoAE/return_normalized_anat_file.m
deleted file mode 100644
index 6a786ac9..00000000
--- a/demos/MoAE/return_normalized_anat_file.m
+++ /dev/null
@@ -1,26 +0,0 @@
-function [anat_normalized_file, anat_range] = return_normalized_anat_file(opt, sub_label)
-  %
-
-  % (C) Copyright 2021 Remi Gau
-
-  [BIDS, opt] = getData(opt, opt.dir.preproc);
-
-  anat_normalized_file = bids.query(BIDS, 'data',  ...
-                                    'modality', 'anat', ...
-                                    'space', 'IXI549Space', ...
-                                    'suffix', 'T1w');
-
-  if isempty(anat_normalized_file)
-    opt.query.space = 'IXI549Space';
-    [anat_normalized_file, anatDataDir] = getAnatFilename(BIDS, opt, sub_label);
-    anat_normalized_file = fullfile(anatDataDir, anat_normalized_file);
-  else
-    anat_normalized_file = anat_normalized_file{1};
-  end
-
-  hdr = spm_vol(anat_normalized_file);
-  vol = spm_read_vols(hdr);
-
-  anat_range = [min(vol(:)) max(vol(:))];
-
-end
diff --git a/src/stats/results/checkMontage.m b/src/stats/results/checkMontage.m
new file mode 100644
index 00000000..72f6aa8b
--- /dev/null
+++ b/src/stats/results/checkMontage.m
@@ -0,0 +1,70 @@
+function [opt, BIDS] = checkMontage(opt, iRes, node, BIDS, subLabel)
+  % 
+  % Check values for create a slice montage.
+  % 
+  % Set default values if they are missing.
+  %
+  % USAGE::
+  %
+  %   [opt, BIDS] = checkMontage(opt, iRes, node, BIDS, subLabel)
+  %
+  %
+
+  % (C) Copyright 2019 bidspm developers
+
+  if nargin < 4
+    BIDS = '';
+    subLabel = '';
+  end
+
+  if isfield(opt.results(iRes), 'montage') && any(opt.results(iRes).montage.do)
+
+    background = opt.results(iRes).montage.background;
+
+    % TODO refactor with getInclusiveMask
+    if isstruct(background)
+
+      if ismember(lower(node.Level), {'run', 'session', 'subject'})
+
+        if isempty(BIDS)
+          BIDS =  bids.layout(opt.dir.preproc, ...
+                              'use_schema', false, ...
+                              'index_dependencies', false, ...
+                              'filter', struct('sub', {opt.subjects}));
+        end
+
+        background.sub = subLabel;
+        background.space = opt.space;
+        file = bids.query(BIDS, 'data', background);
+
+        if iscell(file)
+          if isempty(file)
+            % let checkMaskOrUnderlay figure it out
+            file = '';
+
+          elseif numel(file) == 1
+            file = file{1};
+
+          elseif numel(file) > 1
+            file = file{1};
+
+            msg = sprintf('More than 1 overlay image found for %s.\n Taking the first one.', ...
+                          bids.internal.create_unordered_list(background));
+            id = 'tooManyMontageBackground';
+            logger('WARNING', msg, 'id', id, 'options', opt, 'filename', mfilename());
+          end
+
+        end
+
+        background = file;
+
+      end
+
+    end
+
+    background = checkMaskOrUnderlay(background, opt, 'background');
+    opt.results(iRes).montage.background = background;
+
+  end
+  
+end
diff --git a/src/workflows/stats/bidsResults.m b/src/workflows/stats/bidsResults.m
index e766fbec..9f85f6bb 100644
--- a/src/workflows/stats/bidsResults.m
+++ b/src/workflows/stats/bidsResults.m
@@ -547,62 +547,3 @@
   matlabbatch{end}.result = result;
 
 end
-
-function [opt, BIDS] = checkMontage(opt, iRes, node, BIDS, subLabel)
-
-  if nargin < 4
-    BIDS = '';
-    subLabel = '';
-  end
-
-  if isfield(opt.results(iRes), 'montage') && any(opt.results(iRes).montage.do)
-
-    background = opt.results(iRes).montage.background;
-
-    % TODO refactor with getInclusiveMask
-    if isstruct(background)
-
-      if ismember(lower(node.Level), {'run', 'session', 'subject'})
-
-        if isempty(BIDS)
-          BIDS =  bids.layout(opt.dir.preproc, ...
-                              'use_schema', false, ...
-                              'index_dependencies', false, ...
-                              'filter', struct('sub', {opt.subjects}));
-        end
-
-        background.sub = subLabel;
-        background.space = opt.space;
-        file = bids.query(BIDS, 'data', background);
-
-        if iscell(file)
-          if isempty(file)
-            % let checkMaskOrUnderlay figure it out
-            file = '';
-
-          elseif numel(file) == 1
-            file = file{1};
-
-          elseif numel(file) > 1
-            file = file{1};
-
-            msg = sprintf('More than 1 overlay image found for %s.\n Taking the first one.', ...
-                          bids.internal.create_unordered_list(background));
-            id = 'tooManyMontageBackground';
-            logger('WARNING', msg, 'id', id, 'options', opt, 'filename', mfilename());
-          end
-
-        end
-
-        background = file;
-
-      end
-
-    end
-
-    background = checkMaskOrUnderlay(background, opt, 'background');
-    opt.results(iRes).montage.background = background;
-
-  end
-
-end

From b878771d0fe3d17489be626258c4fcd4d81d91f9 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 5 Mar 2025 14:26:08 +0100
Subject: [PATCH 04/12] ref

---
 src/stats/results/checkMontage.m | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/stats/results/checkMontage.m b/src/stats/results/checkMontage.m
index 72f6aa8b..ecc34e96 100644
--- a/src/stats/results/checkMontage.m
+++ b/src/stats/results/checkMontage.m
@@ -1,7 +1,7 @@
 function [opt, BIDS] = checkMontage(opt, iRes, node, BIDS, subLabel)
-  % 
+  %
   % Check values for create a slice montage.
-  % 
+  %
   % Set default values if they are missing.
   %
   % USAGE::
@@ -66,5 +66,5 @@
     opt.results(iRes).montage.background = background;
 
   end
-  
+
 end

From 6df72957ecfb26a56d8bb5bec4c6aff1acb5decf Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 5 Mar 2025 16:48:33 +0100
Subject: [PATCH 05/12] reuse defaults

---
 demos/MoAE/moae_03_slice_display.m     | 47 +++++++++++++++-----------
 src/defaults/defaultResultsStructure.m |  7 ++--
 2 files changed, 31 insertions(+), 23 deletions(-)

diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index 72b5bc48..84d71e0b 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -47,61 +47,68 @@
 
 opt.results(iRes).montage = setMontage(opt.results(iRes));
 
+opt.results(iRes).sdConfig
+
 % we get the con image to extract data
 ffxDir = getFFXdir(subLabel, opt);
 
 maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
 bf = bids.File(spm_file(maskImage, 'filename'));
-conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
+
 
 %% Layers to put on the figure
 layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
 
 % Layer 1: Anatomical map
-layers(1).color.file = opt.results(iRes).montage.background{1};
+overwrite = true;
+layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
 
-hdr = spm_vol(layers(1).color.file);
-[max_val, min_val] = slover('volmaxmin', hdr);
-layers(1).color.range = [0 max_val];
+% layers(1).color.file = opt.results(iRes).montage.background{1};
+% 
+% hdr = spm_vol(layers(1).color.file);
+% [max_val, min_val] = slover('volmaxmin', hdr);
+% layers(1).color.range = [0 max_val];
 
-layers(1).color.map = gray(256);
 
 %% Layer 2: Dual-coded layer
 %
 %   - contrast estimates color-coded;
+layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
 
+conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
 layers(2).color.file = conImage;
 
 color_map_folder = fullfile(fileparts(which('map_luminance')), '..', 'mat_maps');
-load(fullfile(color_map_folder, 'diverging_bwr_iso.mat'));
+load(fullfile(color_map_folder, layers(2).color.map));
 layers(2).color.map = diverging_bwr;
 
-layers(2).color.range = [-4 4];
-layers(2).color.label = '\beta_{listening} - \beta_{baseline} (a.u.)';
+% layers(2).color.range = [-4 4];
+% layers(2).color.label = '\beta_{listening} - \beta_{baseline} (a.u.)';
 
-%% Layer 2: Dual-coded layer
-%
-%   - t-statistics opacity-coded
 
+%   - t-statistics opacity-coded
 spmTImage = spm_select('FPList', ffxDir, ['^spmT_' bf.entities.label '.nii$']);
 layers(2).opacity.file = spmTImage;
 
-layers(2).opacity.range = [0 3];
-layers(2).opacity.label = '| t |';
+% layers(2).opacity.range = [0 3];
+% layers(2).opacity.label = '| t |';
 
 %% Layer 3 and 4: Contour of ROI
+layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
+
 contour = spm_select('FPList', ffxDir, ['^sub.*' bf.entities.label '.*_mask.nii']);
+
 layers(3).color.file = contour;
-layers(3).color.map = [0 0 0];
-layers(3).color.line_width = 2;
+% layers(3).color.map = [0 0 0];
+% layers(3).color.line_width = 2;
 
 %% Settings
-settings = sd_config_settings('init');
+settings = opt.results(iRes).sdConfig.settings;
 
 % we reuse the details for the SPM montage
-settings.slice.disp_slices = opt.results(1).montage.slices;
-settings.slice.orientation = opt.results(1).montage.orientation;
-settings.fig_specs.n.slice_column = 4;
+% settings.slice.disp_slices = opt.results(1).montage.slices;
+% settings.slice.orientation = opt.results(1).montage.orientation;
+
 settings.fig_specs.title = opt.results(1).name;
 
 %% Display the layers
diff --git a/src/defaults/defaultResultsStructure.m b/src/defaults/defaultResultsStructure.m
index 9bc93fed..aed18634 100644
--- a/src/defaults/defaultResultsStructure.m
+++ b/src/defaults/defaultResultsStructure.m
@@ -33,11 +33,12 @@
 
   layers{2} = struct('color', struct('file', [], ... % con image
                                      'map', 'diverging_bwr_iso', ...
-                                     'range', [-4 4]), ...
-                     'label', '\beta_{listening} - \beta_{baseline} (a.u.)', ...
+                                     'range', [-4 4], ...
+                                     'label', '\beta_{listening} - \beta_{baseline} (a.u.)'), ...
                      'opacity', struct('file', [], ... % spmT image
                                        'range', [2 3], ...
-                                       'label', '| t |'));
+                                       'label', '| t |'), ...
+                     'type', 'dual');
 
   layers{3} = struct('color', struct('file', [], ... % spmT mask thresholded at 0.05 FWD
                                      'map', [0 0 0], ...

From 4f3894757f06e95a0902cbf64e9db8aaba6dbdcf Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 7 Mar 2025 17:54:19 +0100
Subject: [PATCH 06/12] refg

---
 demos/MoAE/moae_03_slice_display.m     | 195 +++++++++++++++----------
 src/defaults/defaultResultsStructure.m |  11 +-
 src/stats/results/renameSpmT.m         |   7 +-
 3 files changed, 129 insertions(+), 84 deletions(-)

diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index 84d71e0b..3f65fc19 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -18,8 +18,6 @@
 
 this_dir = fileparts(mfilename('fullpath'));
 
-subLabel = '01';
-
 opt.pipeline.type = 'stats';
 
 opt.dir.raw = fullfile(this_dir, 'inputs', 'raw');
@@ -31,85 +29,128 @@
 
 opt.model.file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
 
-opt.subjects = [subLabel];
+opt.subjects = {'01'};
 
 % read the model
 opt = checkOptions(opt);
 
-iRes = 1;
-
-opt.results = opt.model.bm.Nodes{iRes}.Model.Software.bidspm.Results{1};
-
-node = opt.model.bm.Nodes{iRes};
-[opt, BIDS] = checkMontage(opt, iRes, node, struct([]), subLabel);
-
-opt = checkOptions(opt);
-
-opt.results(iRes).montage = setMontage(opt.results(iRes));
-
-opt.results(iRes).sdConfig
+% TODO loop over noce and subjects
 
-% we get the con image to extract data
-ffxDir = getFFXdir(subLabel, opt);
-
-maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
-bf = bids.File(spm_file(maskImage, 'filename'));
-
-
-%% Layers to put on the figure
-layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
-
-% Layer 1: Anatomical map
 overwrite = true;
-layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
-
-% layers(1).color.file = opt.results(iRes).montage.background{1};
-% 
-% hdr = spm_vol(layers(1).color.file);
-% [max_val, min_val] = slover('volmaxmin', hdr);
-% layers(1).color.range = [0 max_val];
-
-
-%% Layer 2: Dual-coded layer
-%
-%   - contrast estimates color-coded;
-layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
-
-conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
-layers(2).color.file = conImage;
-
-color_map_folder = fullfile(fileparts(which('map_luminance')), '..', 'mat_maps');
-load(fullfile(color_map_folder, layers(2).color.map));
-layers(2).color.map = diverging_bwr;
-
-% layers(2).color.range = [-4 4];
-% layers(2).color.label = '\beta_{listening} - \beta_{baseline} (a.u.)';
-
-
-%   - t-statistics opacity-coded
-spmTImage = spm_select('FPList', ffxDir, ['^spmT_' bf.entities.label '.nii$']);
-layers(2).opacity.file = spmTImage;
-
-% layers(2).opacity.range = [0 3];
-% layers(2).opacity.label = '| t |';
-
-%% Layer 3 and 4: Contour of ROI
-layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
-
-contour = spm_select('FPList', ffxDir, ['^sub.*' bf.entities.label '.*_mask.nii']);
-
-layers(3).color.file = contour;
-% layers(3).color.map = [0 0 0];
-% layers(3).color.line_width = 2;
-
-%% Settings
-settings = opt.results(iRes).sdConfig.settings;
-
-% we reuse the details for the SPM montage
-% settings.slice.disp_slices = opt.results(1).montage.slices;
-% settings.slice.orientation = opt.results(1).montage.orientation;
-
-settings.fig_specs.title = opt.results(1).name;
 
-%% Display the layers
-[settings, p] = sd_display(layers, settings);
+color_map_folder = fullfile(returnRootDir(), 'lib', 'brain_colours', 'mat_maps');
+
+node = opt.model.bm.Nodes{1};
+
+if any(strcmp(node.Level, {'Run', 'Subject'}))
+    
+    for iSub = 1:numel(opt.subjects)
+        
+        subLabel = opt.subjects{iSub};
+        
+        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 i_name =1:numel(opt.results.name)
+                
+                if opt.results(iRes).binary
+                    layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
+                else
+                    layers = sd_config_layers('init', {'truecolor', 'dual'});
+                end
+                
+                %% Layer 1: Anatomical map
+                layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
+                
+                layers(1).color.file = opt.results(iRes).montage.background{1};
+                
+                hdr = spm_vol(layers(1).color.file);
+                [max_val, min_val] = slover('volmaxmin', hdr);
+                layers(1).color.range = [0 max_val];
+                
+                %% Layer 2: Dual-coded layer
+                
+                % - contrast estimates color-coded;
+                layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
+                
+                name = opt.results.name{i_name};
+                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);
+                
+                if strcmp(stat, 'T')
+                    colorFile = spm_select('FPList', ffxDir, ['^con_' contrastNb '.nii$']);
+                else
+                    colorFile = spm_select('FPList', ffxDir, ['^ess_' contrastNb '.nii$']);
+                end
+                layers(2).color.file = colorFile;
+                
+                title = strrep(name, '_', ' ');
+                layers(2).color.label = [title ' (a.u.)'];
+                
+                % - statistics opacity-coded
+                if strcmp(stat, 'T')
+                    opacityFile = spm_select('FPList', ffxDir, ['^spmT_' contrastNb '.nii$']);
+                    
+                    layers(2).opacity.label = '| t |';
+                    
+                    load(fullfile(color_map_folder, 'diverging_bwr_iso.mat'));
+                    layers(2).color.map = diverging_bwr;
+                else
+                    opacityFile = spm_select('FPList', ffxDir, ['^spmF_' contrastNb '.nii$']);
+                    
+                    layers(2).opacity.label = 'F';
+                    
+                    load(fullfile(color_map_folder, '1hot_iso.mat'));
+                    layers(2).color.map = hot;
+                    
+                    hdr = spm_vol(opacityFile);
+                    [max_val, min_val] = slover('volmaxmin', hdr);
+                    layers(2).color.range = [0 max_val];
+                    
+                    layers(2).opacity.range = [0 5];
+                end
+                layers(2).opacity.file = opacityFile;
+                
+                %% Contour
+                if opt.results(iRes).binary
+                    layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
+                    contour = spm_select('FPList', ffxDir, ['^sub.*' contrastNb '.*_mask.nii']);
+                    layers(3).color.file = contour;
+                end
+                
+                %% Settings
+                settings = opt.results(iRes).sdConfig.settings;
+                
+                % we reuse the details for the SPM montage
+                settings.slice.disp_slices = opt.results(1).montage.slices;
+                settings.slice.orientation = opt.results(1).montage.orientation;
+                
+                settings.fig_specs.title = title;
+                
+                %% Display the layers
+                [settings, p] = sd_display(layers, settings);
+                
+            end
+            
+        end
+        
+    end
+end
\ No newline at end of file
diff --git a/src/defaults/defaultResultsStructure.m b/src/defaults/defaultResultsStructure.m
index aed18634..3a73b988 100644
--- a/src/defaults/defaultResultsStructure.m
+++ b/src/defaults/defaultResultsStructure.m
@@ -32,17 +32,16 @@
   %   load(fullfile(color_map_folder, 'diverging_bwr_iso.mat'));
 
   layers{2} = struct('color', struct('file', [], ... % con image
-                                     'map', 'diverging_bwr_iso', ...
                                      'range', [-4 4], ...
-                                     'label', '\beta_{listening} - \beta_{baseline} (a.u.)'), ...
-                     'opacity', struct('file', [], ... % spmT image
+                                     'label', ''), ...
+                     'opacity', struct('file', [], ... % assume spmT image
                                        'range', [2 3], ...
-                                       'label', '| t |'), ...
+                                       'label', ''), ...
                      'type', 'dual');
 
   layers{3} = struct('color', struct('file', [], ... % spmT mask thresholded at 0.05 FWD
-                                     'map', [0 0 0], ...
-                                     'line_width', 2));
+                                     'map', 'w', ...
+                                     'line_width', 1));
 
   result.sdConfig.layers = layers;
 
diff --git a/src/stats/results/renameSpmT.m b/src/stats/results/renameSpmT.m
index fc715ddb..55881dd6 100644
--- a/src/stats/results/renameSpmT.m
+++ b/src/stats/results/renameSpmT.m
@@ -8,7 +8,10 @@ function renameSpmT(result)
   %
 
   % (C) Copyright 2023 bidspm developers
-  outputFiles = spm_select('FPList', result.dir, '^spmT_[0-9].*_sub-.*nii$');
+  prefixes = {'spmT', 'spmF'};
+  for i_prefix = 1:numel(prefixes)
+      
+  outputFiles = spm_select('FPList', result.dir, ['^' prefixes{i_prefix} '_[0-9].*_sub-.*nii$']);
 
   for iFile = 1:size(outputFiles, 1)
 
@@ -22,4 +25,6 @@ function renameSpmT(result)
 
     movefile(source, target);
   end
+  
+  end
 end

From 8bdc38396caa5154423838140b6f8dff52c41876 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 11 Mar 2025 14:41:00 +0100
Subject: [PATCH 07/12] extract transparent plotting

---
 demos/MoAE/moae_01_bids_app.m          |  18 ++--
 demos/MoAE/moae_03_slice_display.m     | 125 +--------------------
 src/stats/results/transparentMontage.m | 144 +++++++++++++++++++++++++
 src/workflows/stats/bidsResults.m      |   2 +
 4 files changed, 156 insertions(+), 133 deletions(-)
 create mode 100644 src/stats/results/transparentMontage.m

diff --git a/demos/MoAE/moae_01_bids_app.m b/demos/MoAE/moae_01_bids_app.m
index 9fb9289f..41542151 100644
--- a/demos/MoAE/moae_01_bids_app.m
+++ b/demos/MoAE/moae_01_bids_app.m
@@ -119,14 +119,14 @@
 
 VERBOSITY = 3;
 
-bidspm(bids_dir, output_dir, 'subject', ...
-       'participant_label', {subject_label}, ...
-       'action', 'preprocess', ...
-       'task', 'auditory', ...
-       'ignore', {'unwarp', 'slicetiming'}, ...
-       'space', {'IXI549Space'}, ...
-       'fwhm', 6, ...
-       'verbosity', VERBOSITY);
+% bidspm(bids_dir, output_dir, 'subject', ...
+%        'participant_label', {subject_label}, ...
+%        'action', 'preprocess', ...
+%        'task', 'auditory', ...
+%        'ignore', {'unwarp', 'slicetiming'}, ...
+%        'space', {'IXI549Space'}, ...
+%        'fwhm', 6, ...
+%        'verbosity', VERBOSITY);
 
 % ## Stats
 
@@ -164,7 +164,7 @@
 
 bidspm(bids_dir, output_dir, 'subject', ...
        'participant_label', {subject_label}, ...
-       'action', 'stats', ...
+       'action', 'results', ...
        'preproc_dir', preproc_dir, ...
        'model_file', model_file, ...
        'space', {'IXI549Space'}, ...
diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index 3f65fc19..54090dcc 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -20,13 +20,9 @@
 
 opt.pipeline.type = 'stats';
 
-opt.dir.raw = fullfile(this_dir, 'inputs', 'raw');
 opt.dir.derivatives = fullfile(this_dir, 'outputs', 'derivatives');
 opt.dir.preproc = fullfile(opt.dir.derivatives, 'bidspm-preproc');
 
-opt.dir.roi = fullfile(opt.dir.derivatives, 'bidspm-roi');
-opt.dir.stats = fullfile(opt.dir.derivatives, 'bidspm-stats');
-
 opt.model.file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
 
 opt.subjects = {'01'};
@@ -34,123 +30,4 @@
 % read the model
 opt = checkOptions(opt);
 
-% TODO loop over noce and subjects
-
-overwrite = true;
-
-color_map_folder = fullfile(returnRootDir(), 'lib', 'brain_colours', 'mat_maps');
-
-node = opt.model.bm.Nodes{1};
-
-if any(strcmp(node.Level, {'Run', 'Subject'}))
-    
-    for iSub = 1:numel(opt.subjects)
-        
-        subLabel = opt.subjects{iSub};
-        
-        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 i_name =1:numel(opt.results.name)
-                
-                if opt.results(iRes).binary
-                    layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
-                else
-                    layers = sd_config_layers('init', {'truecolor', 'dual'});
-                end
-                
-                %% Layer 1: Anatomical map
-                layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
-                
-                layers(1).color.file = opt.results(iRes).montage.background{1};
-                
-                hdr = spm_vol(layers(1).color.file);
-                [max_val, min_val] = slover('volmaxmin', hdr);
-                layers(1).color.range = [0 max_val];
-                
-                %% Layer 2: Dual-coded layer
-                
-                % - contrast estimates color-coded;
-                layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
-                
-                name = opt.results.name{i_name};
-                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);
-                
-                if strcmp(stat, 'T')
-                    colorFile = spm_select('FPList', ffxDir, ['^con_' contrastNb '.nii$']);
-                else
-                    colorFile = spm_select('FPList', ffxDir, ['^ess_' contrastNb '.nii$']);
-                end
-                layers(2).color.file = colorFile;
-                
-                title = strrep(name, '_', ' ');
-                layers(2).color.label = [title ' (a.u.)'];
-                
-                % - statistics opacity-coded
-                if strcmp(stat, 'T')
-                    opacityFile = spm_select('FPList', ffxDir, ['^spmT_' contrastNb '.nii$']);
-                    
-                    layers(2).opacity.label = '| t |';
-                    
-                    load(fullfile(color_map_folder, 'diverging_bwr_iso.mat'));
-                    layers(2).color.map = diverging_bwr;
-                else
-                    opacityFile = spm_select('FPList', ffxDir, ['^spmF_' contrastNb '.nii$']);
-                    
-                    layers(2).opacity.label = 'F';
-                    
-                    load(fullfile(color_map_folder, '1hot_iso.mat'));
-                    layers(2).color.map = hot;
-                    
-                    hdr = spm_vol(opacityFile);
-                    [max_val, min_val] = slover('volmaxmin', hdr);
-                    layers(2).color.range = [0 max_val];
-                    
-                    layers(2).opacity.range = [0 5];
-                end
-                layers(2).opacity.file = opacityFile;
-                
-                %% Contour
-                if opt.results(iRes).binary
-                    layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
-                    contour = spm_select('FPList', ffxDir, ['^sub.*' contrastNb '.*_mask.nii']);
-                    layers(3).color.file = contour;
-                end
-                
-                %% Settings
-                settings = opt.results(iRes).sdConfig.settings;
-                
-                % we reuse the details for the SPM montage
-                settings.slice.disp_slices = opt.results(1).montage.slices;
-                settings.slice.orientation = opt.results(1).montage.orientation;
-                
-                settings.fig_specs.title = title;
-                
-                %% Display the layers
-                [settings, p] = sd_display(layers, settings);
-                
-            end
-            
-        end
-        
-    end
-end
\ No newline at end of file
+transparentMontage(opt)
diff --git a/src/stats/results/transparentMontage.m b/src/stats/results/transparentMontage.m
new file mode 100644
index 00000000..1e25e94a
--- /dev/null
+++ b/src/stats/results/transparentMontage.m
@@ -0,0 +1,144 @@
+
+function transparentMontage(opt)
+  %
+  % Generate montage with transparent plotting
+  %
+  % USAGE::
+  %
+  %   transparentMontage(opt)
+  %
+  %
+
+  % (C) Copyright 2025 bidspm developers
+
+    overwrite = true;
+    
+    color_map_folder = fullfile(returnRootDir(), 'lib', 'brain_colours', 'mat_maps');
+    
+    for i_node = 1:numel(opt.model.bm.Nodes)
+        
+        node = opt.model.bm.Nodes{i_node};
+    
+    if any(strcmp(node.Level, {'Run', 'Subject'}))
+        
+        for iSub = 1:numel(opt.subjects)
+            
+            subLabel = opt.subjects{iSub};
+            
+            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 i_name =1:numel(opt.results.name)
+                    
+                    if opt.results(iRes).binary
+                        layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
+                    else
+                        layers = sd_config_layers('init', {'truecolor', 'dual'});
+                    end
+                    
+                    %% Layer 1: Anatomical map
+                    layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
+                    
+                    layers(1).color.file = opt.results(iRes).montage.background{1};
+                    
+                    hdr = spm_vol(layers(1).color.file);
+                    [max_val, ~] = slover('volmaxmin', hdr);
+                    layers(1).color.range = [0 max_val];
+                    
+                    %% Layer 2: Dual-coded layer
+                    
+                    % - contrast estimates color-coded;
+                    layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
+                    
+                    name = opt.results.name{i_name};
+                    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);
+                    
+                    if strcmp(stat, 'T')
+                        colorFile = spm_select('FPList', ffxDir, ['^con_' contrastNb '.nii$']);
+                    else
+                        colorFile = spm_select('FPList', ffxDir, ['^ess_' contrastNb '.nii$']);
+                    end
+                    layers(2).color.file = colorFile;
+                    
+                    title = strrep(name, '_', ' ');
+                    layers(2).color.label = [title ' (a.u.)'];
+                    
+                    % - statistics opacity-coded
+                    if strcmp(stat, 'T')
+                        opacityFile = spm_select('FPList', ffxDir, ['^spmT_' contrastNb '.nii$']);
+                        
+                        layers(2).opacity.label = '| t |';
+                        
+                        load(fullfile(color_map_folder, 'diverging_bwr_iso.mat')); %#ok<*LOAD>
+                        layers(2).color.map = diverging_bwr;
+                    else
+                        opacityFile = spm_select('FPList', ffxDir, ['^spmF_' contrastNb '.nii$']);
+                        
+                        layers(2).opacity.label = 'F';
+                        
+                        load(fullfile(color_map_folder, '1hot_iso.mat'));
+                        layers(2).color.map = hot;
+                        
+                        hdr = spm_vol(opacityFile);
+                        [max_val, ~] = slover('volmaxmin', hdr);
+                        layers(2).color.range = [0 max_val];
+                        
+                        layers(2).opacity.range = [0 5];
+                    end
+                    layers(2).opacity.file = opacityFile;
+                    
+                    %% Contour
+                    if opt.results(iRes).binary
+                        layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
+                        contour = spm_select('FPList', ffxDir, ['^sub.*' contrastNb '.*_mask.nii']);
+                        layers(3).color.file = contour;
+                    end
+                    
+                    %% Settings
+                    settings = opt.results(iRes).sdConfig.settings;
+                    
+                    % we reuse the details for the SPM montage
+                    settings.slice.disp_slices = opt.results(1).montage.slices;
+                    settings.slice.orientation = opt.results(1).montage.orientation;
+                    
+                    settings.fig_specs.title = title;
+                    
+                    %% Display the layers
+                    [~, ~, h_figure] = sd_display(layers, settings);
+                    
+                    outputFile = fullfile(ffxDir, [contrastNb '_'  name '.png']);
+                    print(h_figure, outputFile, '-dpng');
+                    close(h_figure)
+                    
+                    % TODO
+                    % rename file
+                    
+                    
+                end
+                
+            end
+            
+        end
+    end
+    end
+    
+end
diff --git a/src/workflows/stats/bidsResults.m b/src/workflows/stats/bidsResults.m
index 9f85f6bb..788a693e 100644
--- a/src/workflows/stats/bidsResults.m
+++ b/src/workflows/stats/bidsResults.m
@@ -271,6 +271,8 @@
 
   cleanUpWorkflow(opt);
 
+  transparentMontage(opt)
+
 end
 
 function [opt, listNodeLevels] = keepRequestedNodes(opt, nodeName, analysisLevel)

From 8663a48762be7cd577e9bca52ade664aeb9b259f Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 11 Mar 2025 14:53:48 +0100
Subject: [PATCH 08/12] ref

---
 demos/MoAE/moae_03_slice_display.m     |   4 +-
 src/stats/results/renameSpmT.m         |  22 +--
 src/stats/results/transparentMontage.m | 258 +++++++++++++------------
 src/workflows/stats/bidsResults.m      |   2 +-
 4 files changed, 143 insertions(+), 143 deletions(-)

diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index 54090dcc..478d82c7 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -28,6 +28,4 @@
 opt.subjects = {'01'};
 
 % read the model
-opt = checkOptions(opt);
-
-transparentMontage(opt)
+opt = chec
\ No newline at end of file
diff --git a/src/stats/results/renameSpmT.m b/src/stats/results/renameSpmT.m
index 55881dd6..9e771681 100644
--- a/src/stats/results/renameSpmT.m
+++ b/src/stats/results/renameSpmT.m
@@ -10,21 +10,21 @@ function renameSpmT(result)
   % (C) Copyright 2023 bidspm developers
   prefixes = {'spmT', 'spmF'};
   for i_prefix = 1:numel(prefixes)
-      
-  outputFiles = spm_select('FPList', result.dir, ['^' prefixes{i_prefix} '_[0-9].*_sub-.*nii$']);
 
-  for iFile = 1:size(outputFiles, 1)
+    outputFiles = spm_select('FPList', result.dir, ['^' prefixes{i_prefix} '_[0-9].*_sub-.*nii$']);
 
-    source = deblank(outputFiles(iFile, :));
+    for iFile = 1:size(outputFiles, 1)
 
-    basename = spm_file(source, 'basename');
-    split = strfind(basename, '_sub');
-    bf = bids.File(basename(split + 1:end));
+      source = deblank(outputFiles(iFile, :));
 
-    target = spm_file(source, 'basename', bf.filename);
+      basename = spm_file(source, 'basename');
+      split = strfind(basename, '_sub');
+      bf = bids.File(basename(split + 1:end));
+
+      target = spm_file(source, 'basename', bf.filename);
+
+      movefile(source, target);
+    end
 
-    movefile(source, target);
-  end
-  
   end
 end
diff --git a/src/stats/results/transparentMontage.m b/src/stats/results/transparentMontage.m
index 1e25e94a..ee6ae7c1 100644
--- a/src/stats/results/transparentMontage.m
+++ b/src/stats/results/transparentMontage.m
@@ -1,4 +1,3 @@
-
 function transparentMontage(opt)
   %
   % Generate montage with transparent plotting
@@ -11,134 +10,137 @@ function transparentMontage(opt)
 
   % (C) Copyright 2025 bidspm developers
 
-    overwrite = true;
-    
-    color_map_folder = fullfile(returnRootDir(), 'lib', 'brain_colours', 'mat_maps');
-    
-    for i_node = 1:numel(opt.model.bm.Nodes)
-        
-        node = opt.model.bm.Nodes{i_node};
-    
+  for i_node = 1:numel(opt.model.bm.Nodes)
+
+    node = opt.model.bm.Nodes{i_node};
+
     if any(strcmp(node.Level, {'Run', 'Subject'}))
-        
-        for iSub = 1:numel(opt.subjects)
-            
-            subLabel = opt.subjects{iSub};
-            
-            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 i_name =1:numel(opt.results.name)
-                    
-                    if opt.results(iRes).binary
-                        layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
-                    else
-                        layers = sd_config_layers('init', {'truecolor', 'dual'});
-                    end
-                    
-                    %% Layer 1: Anatomical map
-                    layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
-                    
-                    layers(1).color.file = opt.results(iRes).montage.background{1};
-                    
-                    hdr = spm_vol(layers(1).color.file);
-                    [max_val, ~] = slover('volmaxmin', hdr);
-                    layers(1).color.range = [0 max_val];
-                    
-                    %% Layer 2: Dual-coded layer
-                    
-                    % - contrast estimates color-coded;
-                    layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
-                    
-                    name = opt.results.name{i_name};
-                    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);
-                    
-                    if strcmp(stat, 'T')
-                        colorFile = spm_select('FPList', ffxDir, ['^con_' contrastNb '.nii$']);
-                    else
-                        colorFile = spm_select('FPList', ffxDir, ['^ess_' contrastNb '.nii$']);
-                    end
-                    layers(2).color.file = colorFile;
-                    
-                    title = strrep(name, '_', ' ');
-                    layers(2).color.label = [title ' (a.u.)'];
-                    
-                    % - statistics opacity-coded
-                    if strcmp(stat, 'T')
-                        opacityFile = spm_select('FPList', ffxDir, ['^spmT_' contrastNb '.nii$']);
-                        
-                        layers(2).opacity.label = '| t |';
-                        
-                        load(fullfile(color_map_folder, 'diverging_bwr_iso.mat')); %#ok<*LOAD>
-                        layers(2).color.map = diverging_bwr;
-                    else
-                        opacityFile = spm_select('FPList', ffxDir, ['^spmF_' contrastNb '.nii$']);
-                        
-                        layers(2).opacity.label = 'F';
-                        
-                        load(fullfile(color_map_folder, '1hot_iso.mat'));
-                        layers(2).color.map = hot;
-                        
-                        hdr = spm_vol(opacityFile);
-                        [max_val, ~] = slover('volmaxmin', hdr);
-                        layers(2).color.range = [0 max_val];
-                        
-                        layers(2).opacity.range = [0 5];
-                    end
-                    layers(2).opacity.file = opacityFile;
-                    
-                    %% Contour
-                    if opt.results(iRes).binary
-                        layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
-                        contour = spm_select('FPList', ffxDir, ['^sub.*' contrastNb '.*_mask.nii']);
-                        layers(3).color.file = contour;
-                    end
-                    
-                    %% Settings
-                    settings = opt.results(iRes).sdConfig.settings;
-                    
-                    % we reuse the details for the SPM montage
-                    settings.slice.disp_slices = opt.results(1).montage.slices;
-                    settings.slice.orientation = opt.results(1).montage.orientation;
-                    
-                    settings.fig_specs.title = title;
-                    
-                    %% Display the layers
-                    [~, ~, h_figure] = sd_display(layers, settings);
-                    
-                    outputFile = fullfile(ffxDir, [contrastNb '_'  name '.png']);
-                    print(h_figure, outputFile, '-dpng');
-                    close(h_figure)
-                    
-                    % TODO
-                    % rename file
-                    
-                    
-                end
-                
-            end
-            
+
+      for iSub = 1:numel(opt.subjects)
+
+        subLabel = opt.subjects{iSub};
+
+        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)
+
+            plotTransparentMontage(opt, SPM, subLabel, iRes, iName);
+
+          end
+
         end
+
+      end
+
     end
-    end
-    
+
+  end
+
+end
+
+function plotTransparentMontage(opt, SPM, subLabel, iRes, iName)
+
+  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
+    layers = sd_config_layers('init', {'truecolor', 'dual'});
+  end
+
+  %% Layer 1: Anatomical map
+  layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
+
+  layers(1).color.file = opt.results(iRes).montage.background{1};
+
+  hdr = spm_vol(layers(1).color.file);
+  [max_val, ~] = slover('volmaxmin', hdr);
+  layers(1).color.range = [0 max_val];
+
+  %% Layer 2: Dual-coded layer
+
+  % - contrast estimates color-coded;
+  layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
+
+  name = opt.results.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
+  if strcmp(stat, 'T')
+    colorFile = spm_select('FPList', ffxDir, ['^con_' contrastNb '.nii$']);
+    opacityFile = spm_select('FPList', ffxDir, ['^spmT_' contrastNb '.nii$']);
+
+    layers(2).opacity.label = '| t |';
+
+    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$']);
+    opacityFile = spm_select('FPList', ffxDir, ['^spmF_' contrastNb '.nii$']);
+
+    layers(2).opacity.label = 'F';
+
+    load(fullfile(color_map_folder, '1hot_iso.mat'));
+    layers(2).color.map = hot;
+
+    hdr = spm_vol(opacityFile);
+    [max_val, ~] = slover('volmaxmin', hdr);
+    layers(2).color.range = [0 max_val];
+
+    layers(2).opacity.range = [0 5];
+  end
+  layers(2).color.file = colorFile;
+  layers(2).opacity.file = opacityFile;
+
+  title = strrep(name, '_', ' ');
+  layers(2).color.label = [title ' (a.u.)'];
+
+  %% Contour
+  if opt.results(iRes).binary
+    layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
+    contour = spm_select('FPList', ffxDir, ['^sub.*' contrastNb '.*_mask.nii']);
+    layers(3).color.file = contour;
+  end
+
+  %% Settings
+  settings = opt.results(iRes).sdConfig.settings;
+
+  % we reuse the details for the SPM montage
+  settings.slice.disp_slices = opt.results(1).montage.slices;
+  settings.slice.orientation = opt.results(1).montage.orientation;
+
+  settings.fig_specs.title = title;
+
+  %% Display the layers
+  [~, ~, h_figure] = sd_display(layers, settings);
+
+  outputFile = fullfile(ffxDir, [contrastNb '_'  name '.png']);
+  print(h_figure, outputFile, '-dpng');
+  close(h_figure);
+
+  % TODO
+  % rename file
+
 end
diff --git a/src/workflows/stats/bidsResults.m b/src/workflows/stats/bidsResults.m
index 788a693e..8ac56e50 100644
--- a/src/workflows/stats/bidsResults.m
+++ b/src/workflows/stats/bidsResults.m
@@ -271,7 +271,7 @@
 
   cleanUpWorkflow(opt);
 
-  transparentMontage(opt)
+  transparentMontage(opt);
 
 end
 

From 0a388b3eb4dffcf565afd64b8a9933c501e9c09b Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 11 Mar 2025 14:54:39 +0100
Subject: [PATCH 09/12] fix

---
 demos/MoAE/moae_03_slice_display.m | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index 478d82c7..79f67205 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -28,4 +28,6 @@
 opt.subjects = {'01'};
 
 % read the model
-opt = chec
\ No newline at end of file
+opt = checkOptions(opt);
+
+transparentMontage(opt);

From 32b9ca16ea838c53085d47db86e77a8b56c37644 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 11 Mar 2025 16:55:25 +0100
Subject: [PATCH 10/12] fix

---
 lib/slice_display                      |  2 +-
 src/bids_model/BidsModel.m             |  1 +
 src/stats/results/transparentMontage.m | 79 ++++++++++++++++++--------
 3 files changed, 58 insertions(+), 24 deletions(-)

diff --git a/lib/slice_display b/lib/slice_display
index 4326779c..f6f1ce42 160000
--- a/lib/slice_display
+++ b/lib/slice_display
@@ -1 +1 @@
-Subproject commit 4326779c8e9d7681e0b13827196aad64c801e170
+Subproject commit f6f1ce42f56ae7bc40e697a1083bc6514a631a9f
diff --git a/src/bids_model/BidsModel.m b/src/bids_model/BidsModel.m
index 0c49baea..65e6ad43 100644
--- a/src/bids_model/BidsModel.m
+++ b/src/bids_model/BidsModel.m
@@ -312,6 +312,7 @@
     end
 
     function results = getResults(obj)
+      %    return results from all nodes
 
       results = struct([]);
       idx = 1;
diff --git a/src/stats/results/transparentMontage.m b/src/stats/results/transparentMontage.m
index ee6ae7c1..d7fb413f 100644
--- a/src/stats/results/transparentMontage.m
+++ b/src/stats/results/transparentMontage.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
@@ -80,7 +110,7 @@ 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
@@ -88,6 +118,7 @@ function plotTransparentMontage(opt, SPM, subLabel, iRes, iName)
   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']);

From 95348ff00ff98d9f30fadf928bc3731fd4a40e50 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 11 Mar 2025 16:58:07 +0100
Subject: [PATCH 11/12] simplify demo

---
 demos/MoAE/moae_03_slice_display.m | 1 -
 1 file changed, 1 deletion(-)

diff --git a/demos/MoAE/moae_03_slice_display.m b/demos/MoAE/moae_03_slice_display.m
index 79f67205..de4847d0 100644
--- a/demos/MoAE/moae_03_slice_display.m
+++ b/demos/MoAE/moae_03_slice_display.m
@@ -27,7 +27,6 @@
 
 opt.subjects = {'01'};
 
-% read the model
 opt = checkOptions(opt);
 
 transparentMontage(opt);

From 6ecc760bf4e329ca465a411fbe5e5757c49ba3a5 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 11 Mar 2025 17:07:28 +0100
Subject: [PATCH 12/12] revert

---
 demos/MoAE/moae_01_bids_app.m | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/demos/MoAE/moae_01_bids_app.m b/demos/MoAE/moae_01_bids_app.m
index 41542151..9fb9289f 100644
--- a/demos/MoAE/moae_01_bids_app.m
+++ b/demos/MoAE/moae_01_bids_app.m
@@ -119,14 +119,14 @@
 
 VERBOSITY = 3;
 
-% bidspm(bids_dir, output_dir, 'subject', ...
-%        'participant_label', {subject_label}, ...
-%        'action', 'preprocess', ...
-%        'task', 'auditory', ...
-%        'ignore', {'unwarp', 'slicetiming'}, ...
-%        'space', {'IXI549Space'}, ...
-%        'fwhm', 6, ...
-%        'verbosity', VERBOSITY);
+bidspm(bids_dir, output_dir, 'subject', ...
+       'participant_label', {subject_label}, ...
+       'action', 'preprocess', ...
+       'task', 'auditory', ...
+       'ignore', {'unwarp', 'slicetiming'}, ...
+       'space', {'IXI549Space'}, ...
+       'fwhm', 6, ...
+       'verbosity', VERBOSITY);
 
 % ## Stats
 
@@ -164,7 +164,7 @@
 
 bidspm(bids_dir, output_dir, 'subject', ...
        'participant_label', {subject_label}, ...
-       'action', 'results', ...
+       'action', 'stats', ...
        'preproc_dir', preproc_dir, ...
        'model_file', model_file, ...
        'space', {'IXI549Space'}, ...