[WIP] update transparent plotting demo

demos/MoAE/moae_03_slice_display.m

@@ -31,33 +31,12 @@
 
 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);
 
-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);
-
-filter.hemi = 'L';
+opt.results = opt.model.bm.Nodes{1}.Model.Software.bidspm.Results{1};
 
-leftRoiFile = bids.query(BIDS_ROI, 'data', filter);
+opt = checkOptions(opt);
 
 % we get the con image to extract data
 ffxDir = getFFXdir(subLabel, opt);
@@ -66,13 +45,12 @@
 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);
 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
@@ -95,25 +73,21 @@
 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
-
-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;
 
-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;