[ENH] add roi based GLM using mars bar

.gitignore

@@ -22,7 +22,7 @@ demos/*/cfg/*.json
 tests/*.png
 tests/group/*
 tests/*/*.json
-tests/dummyData/derivatives/cpp_spm/sub-*/
+tests/dummyData/derivatives/cpp_spm*/sub-*/
 
 # ignore content of the build folder of the doc
 docs/build/*

demos/MoAE/MoAE_run.m

@@ -13,7 +13,7 @@
 % Smoothing to apply
 FWHM = 6;
 
-downloadData = false;
+downloadData = true;
 
 run ../../initCppSpm.m;
 
@@ -23,58 +23,27 @@
 dowload_MoAE_ds(downloadData);
 
 %% Run batches
-% reportBIDS(opt);
-% bidsCopyRawFolder(opt, 1);
+reportBIDS(opt);
+bidsCopyRawFolder(opt, 1);
 
 % In case you just want to run segmentation and skull stripping
-%
-% bidsSegmentSkullStrip(opt);
-%
+
+bidsSegmentSkullStrip(opt);
+
 % NOTE: skull stripping is also included in 'bidsSpatialPrepro'
 
-% bidsSTC(opt);
+bidsSTC(opt);
 
-% bidsSpatialPrepro(opt);
+bidsSpatialPrepro(opt);
 
 % The following do not run on octave for now (because of spmup)
 % anatomicalQA(opt);
 % bidsResliceTpmToFunc(opt);
 % functionalQA(opt);
-%
-% bidsSmoothing(FWHM, opt);
-
-% The following crash on Travis CI
-% bidsFFX('specifyAndEstimate', opt, FWHM);
-% bidsFFX('contrasts', opt, FWHM);
-% bidsResults(opt, FWHM);
-
-%%
-function dowload_MoAE_ds(downloadData)
 
-  if downloadData
+bidsSmoothing(FWHM, opt);
 
-    % URL of the data set to download
-    URL = 'http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip';
-
-    working_directory = fileparts(mfilename('fullpath'));
-
-    % clean previous runs
-    if exist(fullfile(working_directory, 'inputs'), 'dir')
-      rmdir(fullfile(working_directory, 'inputs'), 's');
-    end
-
-    spm_mkdir(fullfile(working_directory, 'inputs'));
-
-    %% Get data
-    fprintf('%-10s:', 'Downloading dataset...');
-    urlwrite(URL, 'MoAEpilot.zip');
-    fprintf(1, ' Done\n\n');
-
-    fprintf('%-10s:', 'Unzipping dataset...');
-    unzip('MoAEpilot.zip');
-    movefile('MoAEpilot', fullfile(working_directory, 'inputs', 'raw'));
-    fprintf(1, ' Done\n\n');
-
-  end
-
-end
+% The following crash on Travis CI
+bidsFFX('specifyAndEstimate', opt, FWHM);
+bidsFFX('contrasts', opt, FWHM);
+bidsResults(opt, FWHM);

demos/MoAE/MoAE_slice_display.m

@@ -59,19 +59,3 @@
 
 %% Display the layers
 [settings, p] = sd_display(layers, settings);
-
-%% Helper function
-function [anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel)
-
-  [BIDS, opt] = getData(opt);
-  [~, anatDataDir] = getAnatFilename(BIDS, subLabel, opt);
-  anat_normalized_file = spm_select('FPList', ...
-                                    anatDataDir, ...
-                                    '^wm.*skullstripped.nii$');
-
-  hdr = spm_vol(anat_normalized_file);
-  vol = spm_read_vols(hdr);
-
-  anatRange = [min(vol(:)) max(vol(:))];
-
-end

demos/MoAE/dowload_MoAE_ds.m

@@ -0,0 +1,31 @@
+% (C) Copyright 2021 Remi Gau
+
+function dowload_MoAE_ds(downloadData)
+
+  if downloadData
+
+    % URL of the data set to download
+    URL = 'http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip';
+
+    working_directory = fileparts(mfilename('fullpath'));
+
+    % clean previous runs
+    if exist(fullfile(working_directory, 'inputs'), 'dir')
+      rmdir(fullfile(working_directory, 'inputs'), 's');
+    end
+
+    spm_mkdir(fullfile(working_directory, 'inputs'));
+
+    %% Get data
+    fprintf('%-10s:', 'Downloading dataset...');
+    urlwrite(URL, 'MoAEpilot.zip');
+    fprintf(1, ' Done\n\n');
+
+    fprintf('%-10s:', 'Unzipping dataset...');
+    unzip('MoAEpilot.zip');
+    movefile('MoAEpilot', fullfile(working_directory, 'inputs', 'raw'));
+    fprintf(1, ' Done\n\n');
+
+  end
+
+end

demos/MoAE/return_normalized_anat_file.m

@@ -0,0 +1,16 @@
+% (C) Copyright 2021 Remi Gau
+
+function [anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel)
+
+  [BIDS, opt] = getData(opt);
+  [~, anatDataDir] = getAnatFilename(BIDS, subLabel, opt);
+  anat_normalized_file = spm_select('FPList', ...
+                                    anatDataDir, ...
+                                    '^wm.*skullstripped.nii$');
+
+  hdr = spm_vol(anat_normalized_file);
+  vol = spm_read_vols(hdr);
+
+  anatRange = [min(vol(:)) max(vol(:))];
+
+end

demos/spm_face_rep/FaceRep_getOption.m

@@ -6,11 +6,10 @@
 
   opt = [];
 
-  % task to analyze
   opt.taskName = 'facerepetition';
 
-  % The directory where the data are located
   opt.dataDir = fullfile(fileparts(mfilename('fullpath')), 'outputs', 'raw');
+  opt.dir.roi = fullfile(opt.dataDir, '..', 'derivatives', 'cpp_spm-roi');
 
   opt.model.hrfDerivatives = [1 1];
 

demos/spm_face_rep/FaceRep_getOptionResults.m

@@ -9,7 +9,7 @@
                             'models', ...
                             'model-faceRepetition_smdl.json');
 
-  opt.glmQA.do = false;
+  opt.glm.QA.do = false;
 
   % Specify the result to compute
   opt.result.Steps(1) = returnDefaultResultsStructure();
@@ -24,17 +24,13 @@
 
   % Specify how you want your output (all the following are on false by default)
   opt.result.Steps(1).Output.png = true();
-
   opt.result.Steps(1).Output.csv = true();
-
   opt.result.Steps(1).Output.thresh_spm = true();
-
   opt.result.Steps(1).Output.binary = true();
 
   % MONTAGE FIGURE OPTIONS
   opt.result.Steps(1).Output.montage.do = true();
   opt.result.Steps(1).Output.montage.slices = -26:3:6; % in mm
-  % axial is default 'sagittal', 'coronal'
   opt.result.Steps(1).Output.montage.orientation = 'axial';
 
 end

demos/spm_face_rep/face_rep_anat.m

@@ -9,7 +9,7 @@
 clear;
 clc;
 
-downloadData = false;
+downloadData = true;
 
 run ../../initCppSpm.m;
 

demos/spm_face_rep/face_rep_func.m

@@ -51,6 +51,7 @@
 bidsSmoothing(FWHM, opt);
 
 % The following crash on Travis CI
+opt.dir.stats = opt.derivativesDir;
 bidsFFX('specifyAndEstimate', opt, FWHM);
 bidsFFX('contrasts', opt, FWHM);
 

demos/spm_face_rep/face_rep_resolution.m

@@ -7,6 +7,7 @@
 
 clear;
 clc;
+close all;
 
 FWHM = 6;
 
@@ -29,6 +30,8 @@
 
 reportBIDS(opt);
 
+modelFile = opt.model.file;
+
 for iResolution = 1:0.5:3
 
   opt.funcVoxelDims = repmat(iResolution, 1, 3);
@@ -39,6 +42,16 @@
                                          'derivatives', ...
                                          ['cpp_spm-res' num2str(iResolution)]), 'cpath');
 
+  content = spm_jsonread(opt.model.file);
+  content.Name = [content.Name, ' resolution - ', num2str(iResolution)];
+
+  p = bids.internal.parse_filename(modelFile);
+  p.model = [p.model, ' resolution', num2str(iResolution)];
+  newModel = spm_file(opt.model.file, 'filename', createFilename(p));
+  opt.model.file = newModel;
+
+  spm_jsonwrite(newModel, content, struct('indent', '   '));
+
   bidsCopyRawFolder(opt, 1);
 
   bidsSTC(opt);

demos/spm_face_rep/face_rep_roi_analysis.m

@@ -11,4 +11,10 @@
 opt.roi.name = {'V1v', 'V1d'};
 opt.roi.space = {'MNI', 'individual'};
 
+opt.dir.stats = fullfile(opt.dataDir, '..', 'derivatives', 'cpp_spm-stats');
+
 bidsCreateROI(opt);
+
+opt.glm.roibased.do = true;
+
+bidsRoiBasedGLM(opt);

demos/spm_face_rep/models/model-faceRepetition_smdl.json

@@ -1,5 +1,5 @@
 {
-   "Name": "face repetition resampling",
+   "Name": "resampling",
    "Description": "model for face repetition to check resampling effects",
    "Input": {
       "task": "facerepetition"
@@ -69,62 +69,6 @@
                "type": "t"
             }
          ]
-      },
-      {
-         "Level": "run",
-         "Transformations": [
-            {
-               "Name": "Factor",
-               "Inputs": [
-                  "trial_type"
-               ]
-            },
-            {
-               "Name": "Convolve",
-               "Model": "spm",
-               "Inputs": [
-                  " "
-               ]
-            }
-         ],
-         "Model": {
-            "X": [
-               "trial_type.F1",
-               "trial_type.F2",
-               "trial_type.N1",
-               "trial_type.N2",
-               "trans_x",
-               "trans_y",
-               "trans_z",
-               "rot_x",
-               "rot_y",
-               "rot_z"
-            ],
-            "Options": {
-               "high_pass_filter_cutoff_secs": 128
-            },
-            "Software": {
-               "SPM": {
-                  "whitening": "FAST"
-               }
-            },
-            "Mask": " "
-         },
-         "AutoContrasts": [
-            "trial_type.F1",
-            "trial_type.F2",
-            "trial_type.N1",
-            "trial_type.N2"
-         ]
-      },
-      {
-         "Level": "dataset",
-         "AutoContrasts": [
-            "trial_type.F1",
-            "trial_type.F2",
-            "trial_type.N1",
-            "trial_type.N2"
-         ]
       }
    ]
 }

miss_hit.cfg

@@ -1,6 +1,6 @@
 # styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
-regex_function_name: "[a-z]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*" # almost anything goes in the root folder
+regex_function_name: "[a-z]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*"
 exclude_dir: "lib"
 copyright_entity: "JH"
 copyright_entity: "DSS"

src/batches/setBatchEstimateModel.m

@@ -60,7 +60,7 @@
   matlabbatch{end}.spm.stats.fmri_est.spmmat = spmMatFile;
 
   writeResiduals = true();
-  if ~opt.glmQA.do
+  if ~opt.glm.QA.do
     writeResiduals = false();
   end
   matlabbatch{end}.spm.stats.fmri_est.write_residuals = writeResiduals;

src/defaults/checkOptions.m

@@ -75,13 +75,17 @@
 
   opt = orderfields(opt);
 
+  opt = setStatsDir(opt);
+
 end
 
 function fieldsToSet = setDefaultOption()
   % this defines the missing fields
 
   fieldsToSet.dataDir = '';
   fieldsToSet.derivativesDir = '';
+  fieldsToSet.dir = struct('raw', '', ...
+                           'derivatives', '');
 
   fieldsToSet.groups = {''};
   fieldsToSet.subjects = {[]};
@@ -113,7 +117,8 @@
   fieldsToSet.model.hrfDerivatives = [0 0];
   fieldsToSet.contrastList = {};
 
-  fieldsToSet.glmQA.do = true;
+  fieldsToSet.glm.QA.do = true;
+  fieldsToSet.glm.roibased.do = false;
 
   % specify the results to compute
   fieldsToSet.result.Steps = returnDefaultResultsStructure();

src/group_level/getRFXdir.m

@@ -32,7 +32,7 @@
   end
 
   rfxDir = fullfile( ...
-                    opt.derivativesDir, ...
+                    opt.dir.stats, ...
                     'group', ...
                     glmDirName);