[FIX] fix and refactor demos, and update help sections

cpp_spm.m

@@ -183,12 +183,22 @@ function cpp_spm(varargin)
     % stats
     opt.dir.preproc = args.Results.preproc_dir;
     opt.model.file = args.Results.model_file;
-    opt.glm.roibased.do = args.Results.roi_based;
+
+    opt = overrideRoiBased(opt, args);
 
   end
 
 end
 
+function opt = overrideRoiBased(opt, args)
+  if isfield(opt, 'glm') && isfield(opt.glm, 'roibased') && ...
+      isfield(opt.glm.roibased, 'do') && opt.glm.roibased.do ~= args.Results.roi_based
+    overrideWarning('roi_based', convertToString(args.Results.roi_based), ...
+                    'glm.roibased.do', convertToString(opt.glm.roibased.do));
+  end
+  opt.glm.roibased.do = args.Results.roi_based;
+end
+
 function opt = overrideDryRun(opt, args)
   if isfield(opt, 'dryRun') && args.Results.dry_run ~= opt.dryRun
     overrideWarning('dry_run', convertToString(args.Results.dry_run), ...

demos/MoAE/Makefile

@@ -33,7 +33,7 @@ $(stats):
 	$(MATLAB) $(ARG) -r "run('moae_01_bids_app.m');exit;"
 
 $(roi): $(stats) moae_03_create_roi_extract_data.m
-	$(MATLAB) $(ARG) -r "run('moae_03_create_roi_extract_data.m');exit;"
+	$(MATLAB) $(ARG) -r "run('moae_02_create_roi_extract_data.m');exit;"
 
 # Octave related recipes
 octave_all: octave_roi
@@ -42,4 +42,4 @@ octave_stats: moae_01_bids_app.m
 	octave $(OCTFLAGS) --eval "run('moae_01_bids_app.m');exit;"
 
 octave_roi: moae_03_create_roi_extract_data.m
-	octave $(OCTFLAGS) --eval "run('moae_03_create_roi_extract_data.m');exit;"
+	octave $(OCTFLAGS) --eval "run('moae_02_create_roi_extract_data.m');exit;"

demos/MoAE/moae_01_bids_app.m

@@ -7,13 +7,11 @@
 % **Preprocessing**
 %
 %   - copies the necessary data from the raw to the derivative folder,
-%   - runs slice time correction
 %   - runs spatial preprocessing
 %
 % those are otherwise handled by the workflows:
 %
 %   - ``bidsCopyInputFolder.m``
-%   - ``bidsSTC.m``
 %   - ``bidsSpatialPrepro.m``
 %
 % **stats**
@@ -51,7 +49,7 @@
 
 %% Dopwnload the dataset
 download_data = false;
-clean = true;
+clean = false;
 download_moae_ds(download_data, clean);
 
 %% PREPROC
@@ -92,6 +90,7 @@
 opt.results(1).csv = true();
 opt.results(1).p = 0.05;
 opt.results(1).MC = 'FWE';
+opt.results(1).binary = true();
 opt.results(1).montage.do = true();
 opt.results(1).montage.background = struct('suffix', 'T1w', ...
                                            'desc', 'preproc', ...

demos/MoAE/moae_02_create_roi_extract_data.m

@@ -15,8 +15,14 @@
 
 subLabel = '01';
 
-opt = moae_get_option_stats();
+opt.dir.derivatives = fullfile(fileparts(mfilename('fullpath')), 'outputs', 'derivatives');
+opt.dir.roi = fullfile(opt.dir.derivatives, 'cpp_spm-roi');
+opt.dir.stats = fullfile(opt.dir.derivatives, 'outputs', 'cpp_spm-stats');
+
+opt.model.file = fullfile(fileparts(mfilename('fullpath')), ...
+                          'models', 'model-MoAE_smdl.json');
 opt.pipeline.type = 'stats';
+
 opt = checkOptions(opt);
 
 %% Get the con image to extract data

demos/MoAE/moae_03_slice_display.m

@@ -8,15 +8,40 @@
 % (C) Copyright 2021 Remi Gau
 
 clear;
+close all;
 clc;
 
 addpath(fullfile(pwd, '..', '..'));
 cpp_spm();
 
+this_dir = fileparts(mfilename('fullpath'));
+
 subLabel = '01';
 
-opt = moae_get_option_stats();
 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, 'cpp_spm-preproc');
+
+opt.dir.roi = fullfile(opt.dir.derivatives, 'cpp_spm-roi');
+opt.dir.stats = fullfile(opt.dir.derivatives, 'cpp_spm-stats');
+
+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');
+
 opt = checkOptions(opt);
 
 use_schema = false;
@@ -85,10 +110,10 @@
 settings = sd_config_settings('init');
 
 % we reuse the details for the SPM montage
-settings.slice.orientation = opt.results(1).Output.montage.orientation;
+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).Contrasts(1).Name;
+settings.fig_specs.title = opt.results(1).name;
 
 %% Display the layers
 [settings, p] = sd_display(layers, settings);

demos/MoAE/moae_denoise_with_glm.m

@@ -1,5 +1,5 @@
 % This script will run the subject level GLM to denoise the data:
-% with no condition in the design matric and only motion confounds.
+% with no condition in the design matrix and only motion confounds.
 %
 % The residuals correspond to the time series of denoised data.
 %
@@ -11,8 +11,16 @@
 addpath(fullfile(pwd, '..', '..'));
 cpp_spm();
 
-opt = moae_get_option_stats();
-opt.model.file = fullfile(pwd, 'models', 'model-denoiseOnly_smdl.json');
+bids_dir = fullfile(fileparts(mfilename('fullpath')), 'inputs', 'raw');
+output_dir = fullfile(bids_dir, '..', '..', 'outputs', 'derivatives');
+preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
+
+model_file = fullfile(pwd, 'models', 'model-denoiseOnly_smdl.json');
+
 opt.glm.keepResiduals = true;
 
-bidsFFX('specifyAndEstimate', opt);
+cpp_spm(bids_dir, output_dir, 'subject', ...
+        'action', 'stats', ...
+        'preproc_dir', preproc_dir, ...
+        'model_file', model_file, ...
+        'options', opt);

demos/MoAE/moae_fmriprep.m

@@ -121,5 +121,6 @@
         'action', 'stats', ...
         'preproc_dir', preproc_dir, ...
         'model_file', model_file, ...
+        'space', {'MNI152NLin6Asym'}, ...
         'fwhm', 8, ...
         'options', opt);

demos/MoAE/models/model-MoAEfmriprep_smdl.json

@@ -5,9 +5,6 @@
   "Input": {
     "task": [
       "auditory"
-    ],
-    "space": [
-      "MNI152NLin6Asym"
     ]
   },
   "Nodes": [

demos/MoAE/models/model-denoiseOnly_smdl.json

@@ -13,15 +13,15 @@
   "Nodes": [
     {
       "Level": "Run",
-      "Name": "run_level",
+      "Name": "denoise",
       "GroupBy": [
         "run",
         "subject"
       ],
       "Model": {
         "X": [
-          "trans_?",
-          "rot_?"
+          "trans_*",
+          "rot_*"
         ],
         "Type": "glm",
         "Options": {

demos/face_repetition/face_rep_02_stats.m

@@ -36,28 +36,26 @@
 addpath(fullfile(pwd, '..', '..'));
 cpp_spm();
 
-bids_dir = fullfile(fileparts(mfilename('fullpath')), 'outputs', 'raw');
-output_dir = fullfile(bids_dir, '..', 'derivatives');
+this_dir = fileparts(mfilename('fullpath'));
+
+bids_dir = fullfile(this_dir, 'outputs', 'raw');
+output_dir = fullfile(this_dir, 'outputs', 'derivatives');
 preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
 
-model_file = fullfile(fileparts(mfilename('fullpath')), ...
-                      'models', ...
-                      'model-faceRepetition_smdl.json');
+model_file = fullfile(this_dir, 'models', 'model-faceRepetition_smdl.json');
 
 subject_label = '01';
 
 % Specify the result to show
 
 % 1rst result to show
 results = defaultResultsStructure();
-results.nodeName = 'run_level';
 
+results.nodeName = 'run_level';
 results.name = 'faces_gt_baseline_1';
 
 % Specify how you want your output
 % (all the following are on false by default)
-results.png = true();
-results.csv = true();
 results.threshSpm = true();
 results.binary = true();
 results.montage.do = true();
@@ -73,7 +71,6 @@
 results = defaultResultsStructure();
 results.nodeName = 'run_level';
 results.name = 'motion';
-results.png = true();
 
 opt.results(2) = results;
 

demos/face_repetition/face_rep_02_stats_parametric.m

@@ -10,23 +10,21 @@
 clear;
 clc;
 
-downloadData = false;
-
 addpath(fullfile(pwd, '..', '..'));
-
 cpp_spm();
 
-%% Gets data and converts it to BIDS
-if downloadData
-  download_face_rep_ds(downloadData);
-end
+this_dir = fileparts(mfilename('fullpath'));
 
-opt = face_rep_get_option_results();
+bids_dir = fullfile(this_dir, 'outputs', 'raw');
+output_dir = fullfile(this_dir, 'outputs', 'derivatives');
+preproc_dir = fullfile(output_dir, 'cpp_spm-preproc');
 
-opt.model.file = spm_file(opt.model.file, 'basename', 'model-faceRepetitionParametric_smdl');
-opt.model.bm = BidsModel('file', opt.model.file);
+model_file = fullfile(this_dir, 'models', 'model-faceRepetitionParametric_smdl.json');
 
-bidsFFX('specifyAndEstimate', opt);
-% bidsFFX('contrasts', opt);
+subject_label = '01';
 
-% bidsResults(opt);
+cpp_spm(bids_dir, output_dir, 'subject', ...
+        'action', 'stats', ...
+        'participant_label', {subject_label}, ...
+        'preproc_dir', preproc_dir, ...
+        'model_file', model_file);

demos/face_repetition/face_rep_03_roi_analysis.m

@@ -14,18 +14,36 @@
 addpath(fullfile(pwd, '..', '..'));
 cpp_spm();
 
-opt = face_rep_get_option_results();
+this_dir = fileparts(mfilename('fullpath'));
+
+%% Create roi
+
+opt.dir.derivatives = fullfile(this_dir, 'outputs', 'derivatives');
+opt.dir.preproc = fullfile(opt.dir.derivatives, 'cpp_spm-preproc');
+opt.dir.roi = fullfile(opt.dir.derivatives, 'cpp_spm-roi');
 
 opt.roi.atlas = 'wang';
 opt.roi.name = {'V1v', 'V1d'};
 opt.roi.space = {'individual'};
 
 bidsCreateROI(opt);
 
-opt.fwhm.func = 0;
-opt.glm.roibased.do = true;
-opt.space = {'individual'};
+%% run GLM
+
+bids_dir = fullfile(this_dir, 'outputs', 'raw');
+output_dir = fullfile(this_dir, 'outputs', 'derivatives');
+preproc_dir = fullfile(opt.dir.derivatives, 'cpp_spm-preproc');
+
 opt.bidsFilterFile.roi.space = 'individual';
 
-bidsFFX('specify', opt);
-bidsRoiBasedGLM(opt);
+model_file = fullfile(this_dir, 'models', 'model-faceRepetition_smdl.json');
+
+cpp_spm(bids_dir, output_dir, 'subject', ...
+        'action', 'stats', ...
+        'participant_label', {'01'}, ...
+        'preproc_dir', preproc_dir, ...
+        'model_file', model_file, ...
+        'roi_based', true, ...
+        'space', {'individual'}, ...
+        'options', opt, ...
+        'fwhm', 0);