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‎demos/MoAE/moae_03_slice_display.m

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -28,6 +28,4 @@
2828
opt.subjects = {'01'};
2929

3030
% read the model
31-
opt = checkOptions(opt);
32-
33-
transparentMontage(opt)
31+
opt = chec

‎src/stats/results/renameSpmT.m

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -10,21 +10,21 @@ function renameSpmT(result)
1010
% (C) Copyright 2023 bidspm developers
1111
prefixes = {'spmT', 'spmF'};
1212
for i_prefix = 1:numel(prefixes)
13-
14-
outputFiles = spm_select('FPList', result.dir, ['^' prefixes{i_prefix} '_[0-9].*_sub-.*nii$']);
1513

16-
for iFile = 1:size(outputFiles, 1)
14+
outputFiles = spm_select('FPList', result.dir, ['^' prefixes{i_prefix} '_[0-9].*_sub-.*nii$']);
1715

18-
source = deblank(outputFiles(iFile, :));
16+
for iFile = 1:size(outputFiles, 1)
1917

20-
basename = spm_file(source, 'basename');
21-
split = strfind(basename, '_sub');
22-
bf = bids.File(basename(split + 1:end));
18+
source = deblank(outputFiles(iFile, :));
2319

24-
target = spm_file(source, 'basename', bf.filename);
20+
basename = spm_file(source, 'basename');
21+
split = strfind(basename, '_sub');
22+
bf = bids.File(basename(split + 1:end));
23+
24+
target = spm_file(source, 'basename', bf.filename);
25+
26+
movefile(source, target);
27+
end
2528

26-
movefile(source, target);
27-
end
28-
2929
end
3030
end

‎src/stats/results/transparentMontage.m

Lines changed: 130 additions & 128 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,3 @@
1-
21
function transparentMontage(opt)
32
%
43
% Generate montage with transparent plotting
@@ -11,134 +10,137 @@ function transparentMontage(opt)
1110

1211
% (C) Copyright 2025 bidspm developers
1312

14-
overwrite = true;
15-
16-
color_map_folder = fullfile(returnRootDir(), 'lib', 'brain_colours', 'mat_maps');
17-
18-
for i_node = 1:numel(opt.model.bm.Nodes)
19-
20-
node = opt.model.bm.Nodes{i_node};
21-
13+
for i_node = 1:numel(opt.model.bm.Nodes)
14+
15+
node = opt.model.bm.Nodes{i_node};
16+
2217
if any(strcmp(node.Level, {'Run', 'Subject'}))
23-
24-
for iSub = 1:numel(opt.subjects)
25-
26-
subLabel = opt.subjects{iSub};
27-
28-
ffxDir = getFFXdir(subLabel, opt);
29-
load(fullfile(ffxDir, 'SPM.mat'))
30-
31-
for iRes = 1:numel(node.Model.Software.bidspm.Results)
32-
33-
opt.results = node.Model.Software.bidspm.Results{iRes};
34-
35-
if ~isfield(opt.results, 'montage') || ~opt.results.montage.do
36-
continue
37-
end
38-
39-
% set defaults
40-
[opt, ~] = checkMontage(opt, iRes, node, struct([]), subLabel);
41-
opt = checkOptions(opt);
42-
opt.results(iRes).montage = setMontage(opt.results(iRes));
43-
44-
for i_name =1:numel(opt.results.name)
45-
46-
if opt.results(iRes).binary
47-
layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
48-
else
49-
layers = sd_config_layers('init', {'truecolor', 'dual'});
50-
end
51-
52-
%% Layer 1: Anatomical map
53-
layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
54-
55-
layers(1).color.file = opt.results(iRes).montage.background{1};
56-
57-
hdr = spm_vol(layers(1).color.file);
58-
[max_val, ~] = slover('volmaxmin', hdr);
59-
layers(1).color.range = [0 max_val];
60-
61-
%% Layer 2: Dual-coded layer
62-
63-
% - contrast estimates color-coded;
64-
layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
65-
66-
name = opt.results.name{i_name};
67-
tmp = struct('name', name);
68-
contrastNb = getContrastNb(tmp, opt, SPM);
69-
70-
% keep track if this is a t test or F test
71-
stat = SPM.xCon(contrastNb).STAT;
72-
73-
contrastNb = sprintf('%04.0f', contrastNb);
74-
75-
if strcmp(stat, 'T')
76-
colorFile = spm_select('FPList', ffxDir, ['^con_' contrastNb '.nii$']);
77-
else
78-
colorFile = spm_select('FPList', ffxDir, ['^ess_' contrastNb '.nii$']);
79-
end
80-
layers(2).color.file = colorFile;
81-
82-
title = strrep(name, '_', ' ');
83-
layers(2).color.label = [title ' (a.u.)'];
84-
85-
% - statistics opacity-coded
86-
if strcmp(stat, 'T')
87-
opacityFile = spm_select('FPList', ffxDir, ['^spmT_' contrastNb '.nii$']);
88-
89-
layers(2).opacity.label = '| t |';
90-
91-
load(fullfile(color_map_folder, 'diverging_bwr_iso.mat')); %#ok<*LOAD>
92-
layers(2).color.map = diverging_bwr;
93-
else
94-
opacityFile = spm_select('FPList', ffxDir, ['^spmF_' contrastNb '.nii$']);
95-
96-
layers(2).opacity.label = 'F';
97-
98-
load(fullfile(color_map_folder, '1hot_iso.mat'));
99-
layers(2).color.map = hot;
100-
101-
hdr = spm_vol(opacityFile);
102-
[max_val, ~] = slover('volmaxmin', hdr);
103-
layers(2).color.range = [0 max_val];
104-
105-
layers(2).opacity.range = [0 5];
106-
end
107-
layers(2).opacity.file = opacityFile;
108-
109-
%% Contour
110-
if opt.results(iRes).binary
111-
layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
112-
contour = spm_select('FPList', ffxDir, ['^sub.*' contrastNb '.*_mask.nii']);
113-
layers(3).color.file = contour;
114-
end
115-
116-
%% Settings
117-
settings = opt.results(iRes).sdConfig.settings;
118-
119-
% we reuse the details for the SPM montage
120-
settings.slice.disp_slices = opt.results(1).montage.slices;
121-
settings.slice.orientation = opt.results(1).montage.orientation;
122-
123-
settings.fig_specs.title = title;
124-
125-
%% Display the layers
126-
[~, ~, h_figure] = sd_display(layers, settings);
127-
128-
outputFile = fullfile(ffxDir, [contrastNb '_' name '.png']);
129-
print(h_figure, outputFile, '-dpng');
130-
close(h_figure)
131-
132-
% TODO
133-
% rename file
134-
135-
136-
end
137-
138-
end
139-
18+
19+
for iSub = 1:numel(opt.subjects)
20+
21+
subLabel = opt.subjects{iSub};
22+
23+
ffxDir = getFFXdir(subLabel, opt);
24+
load(fullfile(ffxDir, 'SPM.mat'));
25+
26+
for iRes = 1:numel(node.Model.Software.bidspm.Results)
27+
28+
opt.results = node.Model.Software.bidspm.Results{iRes};
29+
30+
if ~isfield(opt.results, 'montage') || ~opt.results.montage.do
31+
continue
32+
end
33+
34+
% set defaults
35+
[opt, ~] = checkMontage(opt, iRes, node, struct([]), subLabel);
36+
opt = checkOptions(opt);
37+
opt.results(iRes).montage = setMontage(opt.results(iRes));
38+
39+
for iName = 1:numel(opt.results.name)
40+
41+
plotTransparentMontage(opt, SPM, subLabel, iRes, iName);
42+
43+
end
44+
14045
end
46+
47+
end
48+
14149
end
142-
end
143-
50+
51+
end
52+
53+
end
54+
55+
function plotTransparentMontage(opt, SPM, subLabel, iRes, iName)
56+
57+
overwrite = true;
58+
59+
color_map_folder = fullfile(returnRootDir(), 'lib', 'brain_colours', 'mat_maps');
60+
61+
ffxDir = getFFXdir(subLabel, opt);
62+
63+
if opt.results(iRes).binary
64+
layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
65+
else
66+
layers = sd_config_layers('init', {'truecolor', 'dual'});
67+
end
68+
69+
%% Layer 1: Anatomical map
70+
layers(1) = setFields(layers(1), opt.results(iRes).sdConfig.layers{1}, overwrite);
71+
72+
layers(1).color.file = opt.results(iRes).montage.background{1};
73+
74+
hdr = spm_vol(layers(1).color.file);
75+
[max_val, ~] = slover('volmaxmin', hdr);
76+
layers(1).color.range = [0 max_val];
77+
78+
%% Layer 2: Dual-coded layer
79+
80+
% - contrast estimates color-coded;
81+
layers(2) = setFields(layers(2), opt.results(iRes).sdConfig.layers{2}, overwrite);
82+
83+
name = opt.results.name{iName};
84+
tmp = struct('name', name);
85+
contrastNb = getContrastNb(tmp, opt, SPM);
86+
% keep track if this is a t test or F test
87+
stat = SPM.xCon(contrastNb).STAT;
88+
contrastNb = sprintf('%04.0f', contrastNb);
89+
90+
% - statistics opacity-coded
91+
if strcmp(stat, 'T')
92+
colorFile = spm_select('FPList', ffxDir, ['^con_' contrastNb '.nii$']);
93+
opacityFile = spm_select('FPList', ffxDir, ['^spmT_' contrastNb '.nii$']);
94+
95+
layers(2).opacity.label = '| t |';
96+
97+
load(fullfile(color_map_folder, 'diverging_bwr_iso.mat')); %#ok<*LOAD>
98+
layers(2).color.map = diverging_bwr;
99+
else
100+
colorFile = spm_select('FPList', ffxDir, ['^ess_' contrastNb '.nii$']);
101+
opacityFile = spm_select('FPList', ffxDir, ['^spmF_' contrastNb '.nii$']);
102+
103+
layers(2).opacity.label = 'F';
104+
105+
load(fullfile(color_map_folder, '1hot_iso.mat'));
106+
layers(2).color.map = hot;
107+
108+
hdr = spm_vol(opacityFile);
109+
[max_val, ~] = slover('volmaxmin', hdr);
110+
layers(2).color.range = [0 max_val];
111+
112+
layers(2).opacity.range = [0 5];
113+
end
114+
layers(2).color.file = colorFile;
115+
layers(2).opacity.file = opacityFile;
116+
117+
title = strrep(name, '_', ' ');
118+
layers(2).color.label = [title ' (a.u.)'];
119+
120+
%% Contour
121+
if opt.results(iRes).binary
122+
layers(3) = setFields(layers(3), opt.results(iRes).sdConfig.layers{3}, overwrite);
123+
contour = spm_select('FPList', ffxDir, ['^sub.*' contrastNb '.*_mask.nii']);
124+
layers(3).color.file = contour;
125+
end
126+
127+
%% Settings
128+
settings = opt.results(iRes).sdConfig.settings;
129+
130+
% we reuse the details for the SPM montage
131+
settings.slice.disp_slices = opt.results(1).montage.slices;
132+
settings.slice.orientation = opt.results(1).montage.orientation;
133+
134+
settings.fig_specs.title = title;
135+
136+
%% Display the layers
137+
[~, ~, h_figure] = sd_display(layers, settings);
138+
139+
outputFile = fullfile(ffxDir, [contrastNb '_' name '.png']);
140+
print(h_figure, outputFile, '-dpng');
141+
close(h_figure);
142+
143+
% TODO
144+
% rename file
145+
144146
end

‎src/workflows/stats/bidsResults.m

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -271,7 +271,7 @@
271271

272272
cleanUpWorkflow(opt);
273273

274-
transparentMontage(opt)
274+
transparentMontage(opt);
275275

276276
end
277277

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