Merge pull request #620 from cpp-lln-lab/olf

[ENH] improve group level analysis

cpp_spm.m

@@ -46,6 +46,8 @@ function cpp_spm(varargin)
   addParameter(args, 'preproc_dir', pwd, @isdir);
   addParameter(args, 'model_file', struct([]), isFileOrStruct);
   addParameter(args, 'roi_based', false, isLogical);
+  % group level stats only
+  addParameter(args, 'node_name', '', isChar);
 
   parse(args, varargin{:});
 
@@ -244,20 +246,41 @@ function stats(args)
   opt = checkOptions(opt);
 
   action = args.Results.action;
+  analysisLevel = args.Results.analysis_level;
+  nodeName = args.Results.node_name;
+
+  isSubjectLevel = strcmp(analysisLevel, 'subject');
+  estimate = strcmp(action, 'stats');
+  contrasts = ismember(action, {'stats', 'contrasts'});
+  results = ismember(action, {'stats', 'contrasts', 'results'});
 
   if opt.glm.roibased.do
+
     bidsFFX('specify', opt);
     bidsRoiBasedGLM(opt);
+
   else
-    if strcmp(action, 'stats')
-      bidsFFX('specifyAndEstimate', opt);
+
+    if estimate
+      if isSubjectLevel
+        bidsFFX('specifyAndEstimate', opt);
+      else
+        bidsRFX('RFX', opt, 'nodeName', nodeName);
+      end
     end
-    if ismember(action, {'stats', 'contrasts'})
-      bidsFFX('contrasts', opt);
+
+    if contrasts
+      if isSubjectLevel
+        bidsFFX('contrasts', opt);
+      else
+        bidsRFX('contrasts', opt, 'nodeName', nodeName);
+      end
     end
-    if ismember(action, {'stats', 'contrasts', 'results'})
-      bidsResults(opt);
+
+    if results
+      bidsResults(opt, 'nodeName', nodeName);
     end
+
   end
 
 end

demos/MoAE/moae_01_bids_app.m

@@ -75,6 +75,9 @@
 % Specify how you want your output
 % (all the following are on false by default)
 opt.results(1).png = true();
+opt.results(1).csv = true();
+opt.results(1).p = 0.05;
+opt.results(1).MC = 'none';
 opt.results(1).montage.do = true();
 opt.results(1).montage.background = struct('suffix', 'T1w', ...
                                            'desc', 'preproc', ...

demos/MoAE/models/model-MoAE_smdl.json

@@ -20,13 +20,13 @@
       ],
       "Model": {
         "X": [
-          "trial_type.listening",
+          "condition.listening",
           "trans_?",
           "rot_?"
         ],
         "HRF": {
           "Variables": [
-            "trial_type.listening"
+            "condition.listening"
           ],
           "Model": "spm"
         },
@@ -51,14 +51,14 @@
       "DummyContrasts": {
         "Test": "t",
         "Contrasts": [
-          "trial_type.listening"
+          "condition.listening"
         ]
       },
       "Contrasts": [
         {
           "Name": "listening_inf_baseline",
           "ConditionList": [
-            "trial_type.listening"
+            "condition.listening"
           ],
           "Weights": [
             -1

docs/list_undocumented.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+files=$(find ../src -name "*.m")
+doc_files=$(find ./source -name "*.rst")
+
+echo "${doc_files}"
+
+for file in ${files}; do
+
+    this_file=$(basename "${file}")
+    echo ${this_file}
+
+done

src/WIP/miss_hit.cfg

@@ -0,0 +1,7 @@
+
+# This folder is where we keep things that are not not in use but could prove useful later
+
+metric "cnest": limit 10
+metric "file_length": limit 2000
+metric "cyc": limit 50
+metric "parameters": limit 20

src/batches/stats/setBatchEstimateModel.m

@@ -1,11 +1,11 @@
-function matlabbatch = setBatchEstimateModel(matlabbatch, opt, nodeName, contrastsList)
+function matlabbatch = setBatchEstimateModel(matlabbatch, opt, nodeName, contrastsList, groups)
   %
   % Set up the estimate model batch for run/subject or group level GLM
   %
   % USAGE::
   %
   %   matlabbatch = setBatchEstimateModel(matlabbatch, opt)
-  %   matlabbatch = setBatchEstimateModel(matlabbatch, opt, nodeName, contrastsList)
+  %   matlabbatch = setBatchEstimateModel(matlabbatch, opt, nodeName, contrastsList, groups)
   %
   % :param matlabbatch:
   % :type matlabbatch: structure
@@ -31,8 +31,7 @@
 
       printBatchName('estimate subject level fmri model', opt);
 
-      spmMatFile = cfg_dep( ...
-                           'fMRI model specification SPM file', ...
+      spmMatFile = cfg_dep('fMRI model specification SPM file', ...
                            substruct( ...
                                      '.', 'val', '{}', {1}, ...
                                      '.', 'val', '{}', {1}, ...
@@ -42,17 +41,26 @@
       matlabbatch = returnEstimateModelBatch(matlabbatch, spmMatFile, opt);
 
       % group level
-    case 4
+    case 5
 
       if ischar(contrastsList)
         contrastsList = cellstr(contrastsList);
       end
 
+      if ischar(groups)
+        groups = cellstr(groups);
+      end
+
+      assert(numel(contrastsList) == numel(groups));
+
       printBatchName('estimate group level fmri model', opt);
 
       for j = 1:size(contrastsList)
 
-        spmMatFile = { fullfile(getRFXdir(opt, nodeName, contrastsList{j}), 'SPM.mat') };
+        rfxDir = getRFXdir(opt, nodeName, contrastsList{j}, groups{j});
+        spmMatFile = { fullfile(rfxDir, 'SPM.mat') };
+
+        assert(exist(spmMatFile{1}, 'file') == 0);
 
         % no QA at the group level GLM:
         %   since there is no autocorrelation to check for
@@ -70,6 +78,10 @@
                                                                           'after estimation')));
       end
 
+    otherwise
+
+      error('Should have 2 or 5 inputs...');
+
   end
 
 end