[ENH] add model selection to CLI

bidspm.m

@@ -77,9 +77,12 @@
     case 'default_model'
       cliDefaultModel(varargin{2:end});
 
-    case {'stats', 'contrasts', 'results'}
+    case {'stats', 'contrasts', 'results', 'specify_only'}
       cliStats(varargin{2:end});
 
+    case {'bms'}
+      cliBayesModel(varargin{2:end});
+
     case 'meaning_of_life'
       fprintf('\n42\n\n');
 
@@ -350,7 +353,9 @@ function update()
            'default_model'; ...
            'stats'; ...
            'contrasts'; ...
-           'results'};
+           'results'; ...
+           'specify_only', ...
+           'bms'};
 
 end
 

demos/MoAE/moae_01_bids_app.m

@@ -124,7 +124,7 @@
 bidspm(bids_dir, output_dir, 'subject', ...
        'participant_label', {subject_label}, ...
        'action', 'preprocess', ...
-       'task', {'auditory'}, ...
+       'task', 'auditory', ...
        'ignore', {'unwarp', 'slicetiming'}, ...
        'space', {'IXI549Space'}, ...
        'fwhm', 6, ...

demos/MoAE/test_moae.m

@@ -15,7 +15,7 @@
 clc;
 close all;
 
-download_data = true;
+download_data = false;
 clean = true;
 
 WD = fileparts(mfilename('fullpath'));
@@ -24,7 +24,7 @@
 
 bidspm();
 if download_data
-  download_moae_ds(download_data, clean);
+  download_moae_ds(download_data, clean); %#ok<*UNRCH>
 end
 
 warning('off', 'SPM:noDisplay');
@@ -57,7 +57,7 @@
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', {'01'}, ...
          'action', 'preprocess', ...
-         'task', {'auditory'}, ...
+         'task', 'auditory', ...
          'ignore', ignore{iOption}, ...
          'space', space(iOption), ...
          'options', optionsFile);

demos/bayes/Makefile

@@ -0,0 +1,11 @@
+.PHONY: clean data data_ds000001
+
+data_ds000114:
+	mkdir -p inputs
+	cd inputs && datalad install ///openneuro/ds000114
+	cd inputs && datalad install ///openneuro-derivatives/ds000114-fmriprep
+	cd inputs/ds000114-fmriprep && datalad get sub-*/anat/*MNI152NLin2009cAsym*desc-preproc*.nii.gz -J 12
+	cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*tsv -J 12
+	cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*json -J 12
+	cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*linebisection*MNI152NLin2009cAsym*_mask.nii.gz -J 12
+	cd inputs/ds000114-fmriprep && datalad get sub-*/ses-*/func/*linebisection*MNI152NLin2009cAsym*desc-preproc*bold.nii.gz -J 12

demos/bayes/ds000114_run.m

@@ -0,0 +1,110 @@
+% (C) Copyright 2023 bidspm developers
+
+clear;
+clc;
+
+addpath(fullfile(pwd, '..', '..'));
+bidspm();
+
+% set to false to not re run the smoothing
+SMOOTH = false;
+
+% set to false to not re run the model specification
+FIRST_LEVEL = true;
+
+VERBOSITY = 1;
+
+FWHM = 8;
+
+% to run on fewer subjects
+TESTING = false;
+
+% The directory where the data are located
+root_dir = fileparts(mfilename('fullpath'));
+bids_dir = fullfile(root_dir, 'inputs', 'ds000114');
+fmriprep_dir = fullfile(root_dir, 'inputs', 'ds000114-fmriprep');
+output_dir = fullfile(root_dir, 'outputs', 'ds000114', 'derivatives');
+
+models_dir = fullfile(root_dir, 'models');
+
+participant_label = {'[0-9]*'};
+if TESTING
+  participant_label = {'^0[12]$'};
+end
+
+%% Smooth
+if SMOOTH
+  bidspm(fmriprep_dir, output_dir, 'subject', ...
+         'action', 'smooth', ...
+         'participant_label', participant_label, ...
+         'task', {'overtverbgeneration'}, ...
+         'space', {'MNI152NLin2009cAsym'}, ...
+         'fwhm', FWHM, ...
+         'verbosity', VERBOSITY); %#ok<*UNRCH>
+end
+
+%% create models from a default one
+
+default_model_file = fullfile(models_dir, 'default_model.json');
+% FIXME: crashes with 0 real param
+nb_realignment_param = [6, 24];
+scrubbing = [0, 1];
+
+for i = 1:numel(nb_realignment_param)
+  for j = 1:numel(scrubbing)
+
+    model = bids.util.jsondecode(default_model_file);
+
+    name = sprintf('rp-%i_srub-%i', ...
+                   nb_realignment_param(i), ...
+                   scrubbing(j));
+    model.Name = name;
+    model.Nodes.Name = name;
+
+    design_matrix = model.Nodes.Model.X;
+    if scrubbing(j) == 1
+      design_matrix{end + 1} = '*outlier*'; %#ok<*SAGROW>
+    end
+    switch nb_realignment_param(i)
+      case 0
+      case 6
+        design_matrix{end + 1} = 'rot_?';
+        design_matrix{end + 1} = 'trans_?';
+      case 24
+        design_matrix{end + 1} = 'rot_*';
+        design_matrix{end + 1} = 'trans_*';
+    end
+    model.Nodes.Model.X = design_matrix;
+
+    output_file = fullfile(models_dir, ['model_' name '_smdl.json']);
+    bids.util.jsonencode(output_file, model);
+  end
+end
+
+%% Statistics
+preproc_dir = fullfile(output_dir, 'bidspm-preproc');
+
+%% Subject level analysis
+if FIRST_LEVEL
+
+  opt.glm.useDummyRegressor = true;
+
+  bidspm(bids_dir, output_dir, 'subject', ...
+         'participant_label', participant_label, ...
+         'action', 'specify_only', ...
+         'preproc_dir', preproc_dir, ...
+         'model_file', models_dir, ...
+         'fwhm', FWHM, ...
+         'skip_validation', true, ...
+         'verbosity', VERBOSITY, ...
+         'options', opt);
+
+end
+
+bidspm(bids_dir, output_dir, 'subject', ...
+       'action', 'bms', ...
+       'participant_label', participant_label, ...
+       'models_dir', models_dir, ...
+       'fwhm', FWHM, ...
+       'skip_validation', true, ...
+       'verbosity', VERBOSITY);

demos/bayes/miss_hit.cfg

@@ -0,0 +1,2 @@
+exclude_dir: "inputs"
+exclude_dir: "outputs"

demos/bayes/models/.gitignore

@@ -0,0 +1 @@
+*smdl.json

demos/bayes/models/default_model.json

@@ -0,0 +1,54 @@
+{
+  "Name": "default model",
+  "BIDSModelVersion": "1.0.0",
+  "Description": "FIXME",
+  "Input": {
+    "task": [
+      "overtverbgeneration"
+    ],
+    "space": [
+      "MNI152NLin2009cAsym"
+    ]
+  },
+  "Nodes": [
+    {
+      "Level": "Run",
+      "Name": "FIXME",
+      "GroupBy": [
+        "run",
+        "session",
+        "subject"
+      ],
+      "Model": {
+        "X": [
+          "trial_type.Task",
+          1
+        ],
+        "Type": "glm",
+        "HRF": {
+          "Variables": [
+            "trial_type.Task"
+          ],
+          "Model": "spm"
+        },
+        "Options": {
+          "HighPassFilterCutoffHz": 0.008,
+          "Mask": {
+            "desc": [
+              "brain"
+            ],
+            "suffix": [
+              "mask"
+            ]
+          }
+        },
+        "Software": {
+          "SPM": {
+            "SerialCorrelation": "FAST",
+            "InclusiveMaskingThreshold": 0.8
+          }
+        }
+      }
+    }
+  ]
+}

demos/bayes/spm_my_defaults.m

@@ -0,0 +1,7 @@
+function spm_my_defaults
+  % (C) Copyright 2023 bidspm developers
+  global defaults
+
+  defaults.cmdline = true;
+
+end

demos/face_repetition/face_rep_01_bids_app.m

@@ -52,6 +52,6 @@
 bidspm(bids_dir, output_dir, 'subject', ...
        'participant_label', {subject_label}, ...
        'action', 'preprocess', ...
-       'task', {'facerepetition'}, ...
+       'task', 'facerepetition', ...
        'space', {'individual', 'IXI549Space'}, ...
        'skip_validation', skip_validation);

demos/face_repetition/test_face_rep.m

@@ -66,7 +66,7 @@
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', {'01'}, ...
          'action', 'preprocess', ...
-         'task', {'facerepetition'}, ...
+         'task', 'facerepetition', ...
          'space', {'IXI549Space'}, ...
          'ignore', ignore, ...
          'options', opt, ...

demos/openneuro/Makefile

@@ -60,7 +60,6 @@ data_ds001734:
 	cd inputs/ds001734-fmriprep && datalad get sub-00[1]/func/*json -J 12
 	cd inputs/ds001734-fmriprep && datalad get sub-00[1]/func/*MNI152NLin2009cAsym*desc-preproc*bold.nii.gz -J 12
 
-
 data_ds002799:
 	mkdir -p inputs
 	cd inputs && datalad install ///openneuro/ds002799

demos/openneuro/ds000001_run.m

@@ -18,7 +18,7 @@
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', participant_label(i_participant), ...
          'action', 'preprocess', ...
-         'task', {'balloonanalogrisktask'}, ...
+         'task', 'balloonanalogrisktask', ...
          'space', {'IXI549Space'});
 end
 

demos/openneuro/ds001168_run.m

@@ -32,7 +32,7 @@
 bidspm(bids_dir, output_dir, 'subject', ...
        'participant_label', {'01'}, ...
        'action', 'preprocess', ...
-       'task', {'rest'}, ...
+       'task', 'rest', ...
        'space', {'IXI549Space'}, ...
        'ignore', {'slicetiming'}, ...
        'options', opt);