cpp-lln-lab · Remi-Gau · Mar 5, 2025 · Jun 4, 2020 · Jun 4, 2020 · Jun 4, 2020
diff --git a/.gitmodules b/.gitmodules
@@ -1,7 +1,7 @@
 [submodule "lib/bids-matlab"]
 	path = lib/bids-matlab
 	url = https://github.com/bids-standard/bids-matlab.git
-	branch = dev
+	branch = main
 [submodule "lib/CPP_ROI"]
 	path = lib/CPP_ROI
 	url = https://github.com/cpp-lln-lab/CPP_ROI.git

diff --git a/lib/bids-matlab b/lib/bids-matlab
diff --git a/src/defaults/defaultResultsStructure.m b/src/defaults/defaultResultsStructure.m
@@ -23,4 +23,33 @@
 
   result.nidm = true();
 
+  % tranparent plot
+  layers = struct('color', struct('file', fullfile(spm('dir'), 'canonical', 'avg152T1.nii'), ...
+                                  'range', [0 1], ...
+                                  'map', gray(256)));
+
+  color_map_folder = fullfile(fileparts(which('map_luminance')), '..', 'mat_maps');
+  load(fullfile(color_map_folder, 'diverging_bwr_iso.mat'));
+
+  layers(2) = struct('color', struct('file', [], ... % con image
+                                     'map', diverging_bwr, ...
+                                     'range', [-4 4]), ...
+                                     'label', '\beta_{listening} - \beta_{baseline} (a.u.)', ...
+                     'opacity', struct('file', [], ... % spmT image
+                                       'range', [2 3], ...
+                                       'label', '| t |'));
+
+  layers(3) = struct('color', struct('file', [], ... % spmT mask thresholded at 0.05 FWD
+                                     'map', [0 0 0], ...
+                                     'line_width', 2));
+
+  %% Settings
+  settings = sd_config_settings('init');
+
+  % we reuse the details for the SPM montage
+  settings.slice.orientation = opt.results(1).montage.orientation;
+  settings.slice.disp_slices = -50:10:50;
+  settings.fig_specs.n.slice_column = 4;
+  settings.fig_specs.title = [];
+
 end
+1 −1		.github/workflows/run_examples.yml
+6 −3		.github/workflows/run_tests_matlab.yml
+5 −1		.github/workflows/run_tests_octave.yml
+1 −1		.github/workflows/update_schema.yml
+2 −2		.pre-commit-config.yaml
+1 −1		CITATION.cff
+0 −74		CODE_OF_CONDUCT.md
+35 −296		CONTRIBUTING.md
+8 −4		Makefile
+1 −2		README.md
+ −		docs/__pycache__/utils.cpython-312.pyc
+28 −0		docs/add_links_to_changelog.py
+ −		docs/bids-matlab.pdf
+0 −5		docs/create_manual.sh
+178 −29		docs/source/changelog.md
+6 −0		docs/source/dev_doc.rst
+8 −0		docs/utils.py
+1 −0		miss_hit.cfg
+1 −1		schema.json
+2 −0		tests/test_bids_file.m
+12 −1		tests/test_bids_schema.m
+60 −0		tests/tests_query/test_bids_query_mrs.m
+0 −10		tests/tests_utils/test_create_participants_tsv.m
+8 −7		tests/tests_utils/test_create_readme.m
+0 −8		tests/tests_utils/test_create_scans_tsv.m
+4 −8		tests/tests_utils/test_create_sessions_tsv.m
+1 −5		tests/utils/validate_dataset.m
+1 −1		version.txt