diff --git a/.gitignore b/.gitignore
index 547a6cb5..d520b176 100644
--- a/.gitignore
+++ b/.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/*
diff --git a/demos/MoAE/MoAE_run.m b/demos/MoAE/MoAE_run.m
index ccf8f007..bee7d73d 100644
--- a/demos/MoAE/MoAE_run.m
+++ b/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);
diff --git a/demos/MoAE/MoAE_slice_display.m b/demos/MoAE/MoAE_slice_display.m
index eb7cbe0d..bf370a0c 100644
--- a/demos/MoAE/MoAE_slice_display.m
+++ b/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$');
-
-  hdr = spm_vol(anat_normalized_file);
-  vol = spm_read_vols(hdr);
-
-  anatRange = [min(vol(:)) max(vol(:))];
-
-end
diff --git a/demos/MoAE/dowload_MoAE_ds.m b/demos/MoAE/dowload_MoAE_ds.m
new file mode 100644
index 00000000..f0be3cf9
--- /dev/null
+++ b/demos/MoAE/dowload_MoAE_ds.m
@@ -0,0 +1,31 @@
+% (C) Copyright 2021 Remi Gau
+
+function dowload_MoAE_ds(downloadData)
+
+  if downloadData
+
+    % URL of the data set to download
+    URL = 'http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip';
+
+    working_directory = fileparts(mfilename('fullpath'));
+
+    % clean previous runs
+    if exist(fullfile(working_directory, 'inputs'), 'dir')
+      rmdir(fullfile(working_directory, 'inputs'), 's');
+    end
+
+    spm_mkdir(fullfile(working_directory, 'inputs'));
+
+    %% Get data
+    fprintf('%-10s:', 'Downloading dataset...');
+    urlwrite(URL, 'MoAEpilot.zip');
+    fprintf(1, ' Done\n\n');
+
+    fprintf('%-10s:', 'Unzipping dataset...');
+    unzip('MoAEpilot.zip');
+    movefile('MoAEpilot', fullfile(working_directory, 'inputs', 'raw'));
+    fprintf(1, ' Done\n\n');
+
+  end
+
+end
diff --git a/demos/MoAE/return_normalized_anat_file.m b/demos/MoAE/return_normalized_anat_file.m
new file mode 100644
index 00000000..b6a3627f
--- /dev/null
+++ b/demos/MoAE/return_normalized_anat_file.m
@@ -0,0 +1,16 @@
+% (C) Copyright 2021 Remi Gau
+
+function [anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel)
+
+  [BIDS, opt] = getData(opt);
+  [~, anatDataDir] = getAnatFilename(BIDS, subLabel, opt);
+  anat_normalized_file = spm_select('FPList', ...
+                                    anatDataDir, ...
+                                    '^wm.*skullstripped.nii$');
+
+  hdr = spm_vol(anat_normalized_file);
+  vol = spm_read_vols(hdr);
+
+  anatRange = [min(vol(:)) max(vol(:))];
+
+end
diff --git a/demos/spm_face_rep/FaceRep_getOption.m b/demos/spm_face_rep/FaceRep_getOption.m
index 2db72558..660accd7 100644
--- a/demos/spm_face_rep/FaceRep_getOption.m
+++ b/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];
 
diff --git a/demos/spm_face_rep/FaceRep_getOptionResults.m b/demos/spm_face_rep/FaceRep_getOptionResults.m
index b367b1cd..541fc08a 100644
--- a/demos/spm_face_rep/FaceRep_getOptionResults.m
+++ b/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
diff --git a/demos/spm_face_rep/face_rep_anat.m b/demos/spm_face_rep/face_rep_anat.m
index 2d93eb73..0df75713 100644
--- a/demos/spm_face_rep/face_rep_anat.m
+++ b/demos/spm_face_rep/face_rep_anat.m
@@ -9,7 +9,7 @@
 clear;
 clc;
 
-downloadData = false;
+downloadData = true;
 
 run ../../initCppSpm.m;
 
diff --git a/demos/spm_face_rep/face_rep_func.m b/demos/spm_face_rep/face_rep_func.m
index 4d37afcc..5a104a5b 100644
--- a/demos/spm_face_rep/face_rep_func.m
+++ b/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);
 
diff --git a/demos/spm_face_rep/face_rep_resolution.m b/demos/spm_face_rep/face_rep_resolution.m
index 6db1b455..3e2ec99e 100644
--- a/demos/spm_face_rep/face_rep_resolution.m
+++ b/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);
diff --git a/demos/spm_face_rep/face_rep_roi_analysis.m b/demos/spm_face_rep/face_rep_roi_analysis.m
index 06657e9e..dc8b8af3 100644
--- a/demos/spm_face_rep/face_rep_roi_analysis.m
+++ b/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);
diff --git a/demos/spm_face_rep/models/model-faceRepetition_smdl.json b/demos/spm_face_rep/models/model-faceRepetition_smdl.json
index 45ddda67..29fd68f1 100644
--- a/demos/spm_face_rep/models/model-faceRepetition_smdl.json
+++ b/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"
-         ]
       }
    ]
 }
\ No newline at end of file
diff --git a/lib/CPP_ROI b/lib/CPP_ROI
index 1acf17d7..a53b52aa 160000
--- a/lib/CPP_ROI
+++ b/lib/CPP_ROI
@@ -1 +1 @@
-Subproject commit 1acf17d7b2e5e717e717150e23e6fc0eb0a073b6
+Subproject commit a53b52aa5e971c73b1cf75c2e4a745701d2c28a5
diff --git a/miss_hit.cfg b/miss_hit.cfg
index 2c6a2b5c..bce4b86c 100644
--- a/miss_hit.cfg
+++ b/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"
diff --git a/src/batches/setBatchEstimateModel.m b/src/batches/setBatchEstimateModel.m
index fc6614b1..719e284e 100644
--- a/src/batches/setBatchEstimateModel.m
+++ b/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;
diff --git a/src/defaults/checkOptions.m b/src/defaults/checkOptions.m
index c185732c..e5bb94e1 100644
--- a/src/defaults/checkOptions.m
+++ b/src/defaults/checkOptions.m
@@ -75,6 +75,8 @@
 
   opt = orderfields(opt);
 
+  opt = setStatsDir(opt);
+
 end
 
 function fieldsToSet = setDefaultOption()
@@ -82,6 +84,8 @@
 
   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();
diff --git a/src/group_level/getRFXdir.m b/src/group_level/getRFXdir.m
index 492ee3e2..7a96acba 100644
--- a/src/group_level/getRFXdir.m
+++ b/src/group_level/getRFXdir.m
@@ -32,7 +32,7 @@
   end
 
   rfxDir = fullfile( ...
-                    opt.derivativesDir, ...
+                    opt.dir.stats, ...
                     'group', ...
                     glmDirName);
 
diff --git a/src/setStatsDir.m b/src/setStatsDir.m
new file mode 100644
index 00000000..48aa4072
--- /dev/null
+++ b/src/setStatsDir.m
@@ -0,0 +1,13 @@
+% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
+
+function opt = setStatsDir(opt)
+
+  opt = setDerivativesDir(opt);
+
+  if ~isfield(opt.dir, 'stats')
+    opt.dir.stats = fullfile(opt.derivativesDir, '..', 'cpp_spm-stats');
+  end
+
+  opt.dir.stats = spm_file(opt.dir.stats, 'cpath');
+
+end
diff --git a/src/subject_level/getFFXdir.m b/src/subject_level/getFFXdir.m
index 1825b7be..cad5cb71 100644
--- a/src/subject_level/getFFXdir.m
+++ b/src/subject_level/getFFXdir.m
@@ -25,11 +25,15 @@
     glmDirName = [glmDirName, '_desc-', convertToValidCamelCase(model.Name)];
   end
 
-  ffxDir = fullfile(opt.derivativesDir, ...
+  ffxDir = fullfile(opt.dir.stats, ...
                     ['sub-', subLabel], ...
                     'stats', ...
                     glmDirName);
 
+  if opt.glm.roibased.do
+    ffxDir = [ffxDir '_roi'];
+  end
+
   spm_mkdir(ffxDir);
 
 end
diff --git a/src/templates/bidsTemplateWorkflow.m b/src/templates/bidsTemplateWorkflow.m
new file mode 100644
index 00000000..39721e4c
--- /dev/null
+++ b/src/templates/bidsTemplateWorkflow.m
@@ -0,0 +1,23 @@
+% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
+
+function bidsTemplateWorkflow(opt)
+  %
+  %
+
+  [BIDS, opt] = setUpWorkflow(opt, 'workflow name');
+
+  for iSub = 1:numel(opt.subjects)
+
+    subLabel = opt.subjects{iSub};
+
+    printProcessingSubject(iSub, subLabel);
+
+    matlabbatch = [];
+
+    %     matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel);
+
+    saveAndRunWorkflow(matlabbatch, 'workflow name', opt, subLabel);
+
+  end
+
+end
diff --git a/src/workflows/bidsCreateROI.m b/src/workflows/bidsCreateROI.m
index 0b8fc0db..2349c503 100644
--- a/src/workflows/bidsCreateROI.m
+++ b/src/workflows/bidsCreateROI.m
@@ -8,16 +8,18 @@ function bidsCreateROI(opt)
 
   [BIDS, opt] = setUpWorkflow(opt, 'create ROI');
 
-  opt.roiDir = [opt.derivativesDir '-roi'];
+  opt.dir.roi = [opt.derivativesDir '-roi'];
   spm_mkdir(fullfile(opt.roiDir, 'group'));
 
+  opt.jobsDir = fullfile(opt.dir.roi, 'JOBS', opt.taskName);
+
   hemi = {'lh', 'rh'};
 
   for iHemi = 1:numel(hemi)
 
     for iROI = 1:numel(opt.roi.name)
 
-      extractRoiFromAtlas(fullfile(opt.roiDir, 'group'), ...
+      extractRoiFromAtlas(fullfile(opt.dir.roi, 'group'), ...
                           opt.roi.atlas, ...
                           opt.roi.name{iROI}, ...
                           hemi{iHemi});
@@ -55,7 +57,7 @@ function bidsCreateROI(opt)
       saveAndRunWorkflow(matlabbatch, 'inverseNormalize', opt, subLabel);
 
       %% move and rename file
-      spm_mkdir(opt.roiDir, ['sub-' subLabel], 'roi');
+      spm_mkdir(opt.dir.roi, ['sub-' subLabel], 'roi');
 
       roiList = spm_select('FPlist', ...
                            fullfile(opt.roiDir, 'group'), ...
@@ -78,7 +80,8 @@ function bidsCreateROI(opt)
         newName = createFilename(nameStructure);
 
         movefile(roiImage, ...
-                 fullfile(opt.roiDir, ['sub-' subLabel], 'roi', newName));
+                 fullfile(opt.dir.roi, ['sub-' subLabel], 'roi', newName));
+
       end
 
     end
diff --git a/src/workflows/bidsFFX.m b/src/workflows/bidsFFX.m
index a56f5f95..5765e289 100644
--- a/src/workflows/bidsFFX.m
+++ b/src/workflows/bidsFFX.m
@@ -27,9 +27,19 @@ function bidsFFX(action, opt, funcFWHM)
   % For unsmoothed data ``funcFWHM = 0``, for smoothed data ``funcFWHM = ... mm``.
   % In this way we can make multiple ffx for different smoothing degrees.
   %
+  
+  if opt.glm.roibased.do
+      message = sprintf(...
+          ['The option opt.glm.roibased.do is set to true.\n', ...
+           ' Change the option to false to use this workflow or\n', ...
+           ' use the bidsRoiBasedGLM workflow to run roi based GLM.']);
+      error(message);
+  end  
 
   [BIDS, opt] = setUpWorkflow(opt, 'subject level GLM');
 
+  opt.jobsDir = fullfile(opt.dir.stats, 'JOBS', opt.taskName);
+
   if isempty(opt.model.file)
     opt = createDefaultModel(BIDS, opt);
   end
@@ -76,7 +86,7 @@ function bidsFFX(action, opt, funcFWHM)
 
         saveAndRunWorkflow(matlabbatch, batchName, opt, subLabel);
 
-        if opt.glmQA.do
+        if opt.glm.QA.do
           plot_power_spectra_of_GLM_residuals( ...
                                               getFFXdir(subLabel, funcFWHM, opt), ...
                                               opt.metadata.RepetitionTime);
diff --git a/src/workflows/bidsRFX.m b/src/workflows/bidsRFX.m
index f72fde14..a735c538 100644
--- a/src/workflows/bidsRFX.m
+++ b/src/workflows/bidsRFX.m
@@ -41,6 +41,8 @@ function bidsRFX(action, opt, funcFWHM, conFWHM)
 
   [~, opt] = setUpWorkflow(opt, 'group level GLM');
 
+  opt.jobsDir = fullfile(opt.dir.stats, 'JOBS', opt.taskName);
+
   switch action
 
     case 'smoothContrasts'
diff --git a/src/workflows/bidsRoiBasedGLM.m b/src/workflows/bidsRoiBasedGLM.m
new file mode 100644
index 00000000..fdc02688
--- /dev/null
+++ b/src/workflows/bidsRoiBasedGLM.m
@@ -0,0 +1,123 @@
+% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
+
+function bidsRoiBasedGLM(opt)
+  %
+  %
+  
+  if ~opt.glm.roibased.do
+      message = sprintf(...
+          ['The option opt.glm.roibased.do is set to false.\n', ...
+           ' Change the option to true to use this workflow or\n', ...
+           ' use the bidsFFX workflow to run whole brain GLM.']);
+      error(message);
+  end
+
+  funcFWHM = 0;
+
+  [BIDS, opt] = setUpWorkflow(opt, 'roi based glm');
+
+  opt.space = 'individual';
+  opt.jobsDir = fullfile(opt.dir.stats, 'JOBS', opt.taskName);
+
+  if isempty(opt.model.file)
+    opt = createDefaultModel(BIDS, opt);
+  end
+
+  for iSub = 1:numel(opt.subjects)
+
+    subLabel = opt.subjects{iSub};
+
+    printProcessingSubject(iSub, subLabel);
+
+    matlabbatch = [];
+
+    matlabbatch = setBatchSubjectLevelGLMSpec(matlabbatch, BIDS, opt, subLabel, funcFWHM);
+
+    batchName = ['specify_roi_based_GLM_task-', opt.taskName];
+
+    saveAndRunWorkflow(matlabbatch, batchName, opt, subLabel);
+
+    load(fullfile(getFFXdir(subLabel, funcFWHM, opt), 'SPM.mat'));
+
+    nbRuns = numel(SPM.Sess);
+
+    conditions = {};
+    runs = [];
+    durations = [];
+    for iRun = 1:nbRuns
+      tmp = cat(2, SPM.Sess(iRun).U(:).name);
+      conditions = cat(2, conditions,  tmp);
+      runs = [runs ones(size(tmp)) * iRun];
+      for iCdt = 1:numel(tmp)
+        durations = [durations mean(SPM.Sess(iRun).U(iCdt).dur)];
+      end
+    end
+
+    names = unique(conditions);
+    events = [];
+    for iEvent = 1:numel(conditions)
+      events(end + 1) = find(strcmp(conditions(iEvent), names));
+    end
+
+    roiList = spm_select('FPList', ...
+                         fullfile(opt.dir.roi, ['sub-' subLabel], 'roi'), ...
+                         '^sub-.*_mask.nii$');
+
+    model = mardo(SPM);
+
+    for iROI = 1:size(roiList, 1)
+
+      roiImage = deblank(roiList(iROI, :));
+
+      % create ROI object for Marsbar
+      % and convert to matrix format to avoid delicacies of image format
+      roiObject = maroi_image(struct( ...
+                                     'vol', spm_vol(roiImage), ...
+                                     'binarize', true, ...
+                                     'func', []));
+      roiObject = maroi_matrix(roiObject);
+
+      % Extract data and do MarsBaR estimation
+      data = get_marsy(roiObject, model, 'mean');
+      estimation = estimate(model, data);
+
+      % -------------------- IMPROVE ------------------------ %
+
+      % currently this only computes this averages over all all events
+      % we will want to use the bids model to know which event to fit
+      % based on the contrasts.
+
+      % Fitted time courses
+      [tc, dt] = event_fitted(estimation, [runs; events], durations);
+
+      % Get percent signal change
+      psc = event_signal(estimation, [runs; events], durations, 'abs max');
+
+      % -------------------- IMPROVE ------------------------ %
+
+      p = bids.internal.parse_filename(spm_file(roiImage, 'filename'));
+      fields = {'hemi', 'desc', 'label'};
+      for iField = 1:numel(fields)
+        if ~isfield(p, fields{iField})
+          p.(fields{iField}) = '';
+        end
+      end
+      nameStructure = struct( ...
+                             'sub', subLabel, ...
+                             'task', opt.taskName, ...
+                             'space', 'individual', ...
+                             'hemi', p.hemi, ...
+                             'desc', p.desc, ...
+                             'label', p.label, ...
+                             'type', 'estimates', ...
+                             'ext', '.mat');
+      newName = createFilename(nameStructure);
+
+      save(fullfile(getFFXdir(subLabel, funcFWHM, opt), newName), ...
+           'estimation', 'tc', 'dt', 'psc');
+
+    end
+
+  end
+
+end
diff --git a/tests/createDummyDataSet.sh b/tests/createDummyDataSet.sh
index 5b7bc3f7..d38a692e 100755
--- a/tests/createDummyDataSet.sh
+++ b/tests/createDummyDataSet.sh
@@ -4,24 +4,28 @@
 
 # defines where the BIDS data set will be created
 StartDir=`pwd` # relative to starting directory
-StartDir=$StartDir/dummyData/derivatives/cpp_spm
+PrerpoDir=$StartDir/dummyData/derivatives/cpp_spm
+StatsDir=$StartDir/dummyData/derivatives/cpp_spm-stats
+
+mkdir $StatsDir
 
 SubList='ctrl01 ctrl02 blind01 blind02 01 02' # subject list
 SesList='01 02' # session list
 
-for Subject in $SubList # loop through subjects
+for Subject in $SubList
 do
 
-		mkdir $StartDir/sub-$Subject # create folder for subject
+		mkdir $PrerpoDir/sub-$Subject
+		mkdir $StatsDir/sub-$Subject
 
-		for Ses in $SesList # loop through sessions
+		for Ses in $SesList
 		do
 
 			# create folder for each session and functional and fmap
-			mkdir $StartDir/sub-$Subject/ses-$Ses
+			mkdir $PrerpoDir/sub-$Subject/ses-$Ses
 
 			# FUNC
-			ThisDir=$StartDir/sub-$Subject/ses-$Ses/func
+			ThisDir=$PrerpoDir/sub-$Subject/ses-$Ses/func
 			mkdir $ThisDir
 
 			touch $ThisDir/sub-$Subject\_ses-$Ses\_task-vismotion_run-1_bold.nii
@@ -57,7 +61,7 @@ do
 			echo "6\t2\tVisMotUp" >> $ThisDir/sub-$Subject\_ses-$Ses\_task-vismotion_run-2_events.tsv
 
 			# FMAP
-			ThisDir=$StartDir/sub-$Subject/ses-$Ses/fmap
+			ThisDir=$PrerpoDir/sub-$Subject/ses-$Ses/fmap
 			mkdir $ThisDir
 
 			touch $ThisDir/sub-$Subject\_ses-$Ses\_run-1_phasediff.nii
@@ -82,7 +86,7 @@ do
 		done
 
 		# ANAT
-		ThisDir=$StartDir/sub-$Subject/ses-01/anat
+		ThisDir=$PrerpoDir/sub-$Subject/ses-01/anat
 		mkdir $ThisDir
 
 		touch $ThisDir/sub-$Subject\_ses-01_T1w.nii
@@ -93,8 +97,8 @@ do
 		touch $ThisDir/c3sub-$Subject\_ses-01_T1w.nii
 
 		# STATS
-		mkdir $StartDir/sub-$Subject/stats
-		ThisDir=$StartDir/sub-$Subject/stats/task-vismotion_space-MNI_FWHM-6
+		mkdir $StatsDir/sub-$Subject/stats
+		ThisDir=$StatsDir/sub-$Subject/stats/task-vismotion_space-MNI_FWHM-6
 		mkdir $ThisDir
 
 		cp dummyData/SPM.mat $ThisDir/SPM.mat
diff --git a/tests/test_bidsCopyRawFolder.m b/tests/test_bidsCopyRawFolder.m
index 523c96bb..a86801ad 100644
--- a/tests/test_bidsCopyRawFolder.m
+++ b/tests/test_bidsCopyRawFolder.m
@@ -12,8 +12,6 @@ function test_bidsCopyRawFolderBasic()
 
   opt = setOptions('MoAE');
 
-  opt = checkOptions(opt);
-
   bidsCopyRawFolder(opt, 1);
 
   layoutRaw = bids.layout(opt.dataDir);
@@ -52,8 +50,6 @@ function test_bidsCopyRawFolder2tasks()
 
   opt.taskName = 'vismotion';
 
-  opt = checkOptions(opt);
-
   unZip = false;
   deleteZippedNii = false;
   bidsCopyRawFolder(opt, deleteZippedNii, {'func'}, unZip);
diff --git a/tests/test_checkOptions.m b/tests/test_checkOptions.m
index a8ae7db1..071e62bf 100644
--- a/tests/test_checkOptions.m
+++ b/tests/test_checkOptions.m
@@ -13,8 +13,7 @@ function test_checkOptionsBasic()
   opt.taskName = 'testTask';
   opt = checkOptions(opt);
 
-  expectedOptions = defaultOptions();
-  expectedOptions.taskName = 'testTask';
+  expectedOptions = defaultOptions('testTask');
 
   assertEqual(opt, expectedOptions);
 
diff --git a/tests/test_createAndReturnOnsetFile.m b/tests/test_createAndReturnOnsetFile.m
index d23ec58f..d013bc70 100644
--- a/tests/test_createAndReturnOnsetFile.m
+++ b/tests/test_createAndReturnOnsetFile.m
@@ -16,7 +16,6 @@ function test_createAndReturnOnsetFileBasic()
   iRun = 1;
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
@@ -28,7 +27,7 @@ function test_createAndReturnOnsetFileBasic()
   onsetFileName = createAndReturnOnsetFile(opt, subLabel, tsvFile, funcFWHM);
 
   expectedFileName = fullfile(fileparts(mfilename('fullpath')), ...
-                              'dummyData', 'derivatives', 'cpp_spm', 'sub-01', 'stats', ...
+                              'dummyData', 'derivatives', 'cpp_spm-stats', 'sub-01', 'stats', ...
                               'task-vislocalizer_space-MNI_FWHM-6', ...
                               'sub-01_ses-01_task-vislocalizer_space-MNI_onsets.mat');
 
diff --git a/tests/test_createDefaultModel.m b/tests/test_createDefaultModel.m
index f95e98a3..bf08364d 100644
--- a/tests/test_createDefaultModel.m
+++ b/tests/test_createDefaultModel.m
@@ -12,8 +12,6 @@ function test_createDefaultModelBasic()
 
   opt = setOptions('vislocalizer');
 
-  opt = checkOptions(opt);
-
   [BIDS, opt] = getData(opt);
 
   createDefaultModel(BIDS, opt);
diff --git a/tests/test_getAnatFilename.m b/tests/test_getAnatFilename.m
index 7cebdfd0..05098182 100644
--- a/tests/test_getAnatFilename.m
+++ b/tests/test_getAnatFilename.m
@@ -20,8 +20,6 @@ function test_getAnatFilenameBasic()
 
   opt = setOptions('vislocalizer', subLabel);
 
-  opt = checkOptions(opt);
-
   [BIDS, opt] = getData(opt);
 
   [anatImage, anatDataDir] = getAnatFilename(BIDS, subLabel, opt);
diff --git a/tests/test_getBoldFilename.m b/tests/test_getBoldFilename.m
index 9ea0c257..ee3aa79a 100644
--- a/tests/test_getBoldFilename.m
+++ b/tests/test_getBoldFilename.m
@@ -17,8 +17,6 @@ function test_getBoldFilenameBasic()
 
   opt = setOptions('vislocalizer', subLabel);
 
-  opt = checkOptions(opt);
-
   [BIDS, opt] = getData(opt);
 
   opt.query = struct('acq', '');
diff --git a/tests/test_getBoldFilenameForFFX.m b/tests/test_getBoldFilenameForFFX.m
index f677e761..63675f46 100644
--- a/tests/test_getBoldFilenameForFFX.m
+++ b/tests/test_getBoldFilenameForFFX.m
@@ -17,8 +17,6 @@ function test_getBoldFilenameForFFXBasic()
 
   opt = setOptions('vislocalizer', subLabel);
 
-  opt = checkOptions(opt);
-
   [BIDS, opt] = getData(opt);
 
   [boldFileName, prefix] = getBoldFilenameForFFX(BIDS, opt, subLabel, funcFWHM, iSes, iRun);
diff --git a/tests/test_getData.m b/tests/test_getData.m
index dfa32545..6cbd66c4 100644
--- a/tests/test_getData.m
+++ b/tests/test_getData.m
@@ -13,7 +13,6 @@ function test_getDataMetadata()
   subLabel = '01';
 
   opt = setOptions('vismotion', subLabel);
-  opt = checkOptions(opt);
 
   [~, opt] = getData(opt, [], 'T1w');
 
@@ -24,7 +23,6 @@ function test_getDataMetadata()
 function test_getDataErrorTask()
 
   opt = setOptions('testTask');
-  opt = checkOptions(opt);
 
   assertExceptionThrown( ...
                         @()getData(opt), ...
diff --git a/tests/test_getFFXdir.m b/tests/test_getFFXdir.m
index 61440e96..1e0c4005 100644
--- a/tests/test_getFFXdir.m
+++ b/tests/test_getFFXdir.m
@@ -14,11 +14,9 @@ function test_getFFXdirBasic()
   subLabel = '01';
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   expectedOutput = fullfile(fileparts(mfilename('fullpath')), 'dummyData', 'derivatives', ...
-                            'cpp_spm', 'sub-01', 'stats', ...
+                            'cpp_spm-stats', 'sub-01', 'stats', ...
                             'task-vislocalizer_space-MNI_FWHM-0');
 
   ffxDir = getFFXdir(subLabel, funcFWFM, opt);
@@ -34,13 +32,11 @@ function test_getFFXdirUserSpecified()
 
   opt = setOptions('nback', subLabel);
   opt.space = 'individual';
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   ffxDir = getFFXdir(subLabel, funcFWHM, opt);
 
   expectedOutput = fullfile(fileparts(mfilename('fullpath')), 'dummyData', 'derivatives', ...
-                            'cpp_spm', 'sub-02', 'stats', ...
+                            'cpp_spm-stats', 'sub-02', 'stats', ...
                             'task-nback_space-individual_FWHM-6_desc-nbackMVPA');
 
   assertEqual(exist(expectedOutput, 'dir'), 7);
diff --git a/tests/test_getMeanFuncFilename.m b/tests/test_getMeanFuncFilename.m
index 623c1ec1..c5bf35ef 100644
--- a/tests/test_getMeanFuncFilename.m
+++ b/tests/test_getMeanFuncFilename.m
@@ -13,7 +13,6 @@ function test_getMeanFuncFilenameBasic()
   subLabel = '01';
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
diff --git a/tests/test_getRFXdir.m b/tests/test_getRFXdir.m
index 9fa507c3..c59f51a9 100644
--- a/tests/test_getRFXdir.m
+++ b/tests/test_getRFXdir.m
@@ -14,8 +14,6 @@ function test_getRFXdirBasic()
   conFWHM = 0;
 
   opt = setOptions('vislocalizer');
-  opt = checkOptions(opt);
-  opt = setDerivativesDir(opt);
 
   rfxDir = getRFXdir(opt, funcFWHM, conFWHM);
 
@@ -23,7 +21,7 @@ function test_getRFXdirBasic()
                             fileparts(mfilename('fullpath')), ...
                             'dummyData', ...
                             'derivatives', ...
-                            'cpp_spm', ...
+                            'cpp_spm-stats', ...
                             'group', ...
                             'task-vislocalizer_space-MNI_FWHM-0_conFWHM-0');
 
@@ -37,8 +35,6 @@ function test_getFFXdirUserSpecified()
   funcFWHM = 6;
 
   opt = setOptions('nback');
-  opt = checkOptions(opt);
-  opt = setDerivativesDir(opt);
 
   rfxDir = getRFXdir(opt, funcFWHM, conFWHM);
 
@@ -46,7 +42,7 @@ function test_getFFXdirUserSpecified()
                             fileparts(mfilename('fullpath')), ...
                             'dummyData', ...
                             'derivatives', ...
-                            'cpp_spm', ...
+                            'cpp_spm-stats', ...
                             'group', ...
                             'task-nback_space-MNI_FWHM-6_conFWHM-0_desc-nbackMVPA');
 
diff --git a/tests/test_getRealignParamFile.m b/tests/test_getRealignParamFile.m
index 9ebce4ea..a71a9070 100644
--- a/tests/test_getRealignParamFile.m
+++ b/tests/test_getRealignParamFile.m
@@ -15,7 +15,6 @@ function test_getRealignParamFileBasic()
   run = '';
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
@@ -39,7 +38,6 @@ function test_getRealignParamFileNativeSpace()
 
   opt = setOptions('vislocalizer', subLabel);
   opt.space = 'individual';
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
@@ -63,7 +61,6 @@ function test_getRealignParamFileFFX()
   iRun = 1;
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
diff --git a/tests/test_loadAndCheckOptions.m b/tests/test_loadAndCheckOptions.m
index ba2dc50f..c06e2bb8 100644
--- a/tests/test_loadAndCheckOptions.m
+++ b/tests/test_loadAndCheckOptions.m
@@ -21,8 +21,7 @@ function test_loadAndCheckOptionsBasic()
   % makes sure that it is picked up by default
   opt = loadAndCheckOptions();
 
-  expectedOptions = defaultOptions();
-  expectedOptions.taskName = 'vismotion';
+  expectedOptions = defaultOptions('vismotion');
 
   assertEqual(opt, expectedOptions);
 
@@ -39,8 +38,7 @@ function test_loadAndCheckOptionsStructure()
   % makes sure that it is picked up by default
   opt = loadAndCheckOptions(opt);
 
-  expectedOptions = defaultOptions();
-  expectedOptions.taskName = 'vismotion';
+  expectedOptions = defaultOptions('vismotion');
 
   assertEqual(opt, expectedOptions);
 
@@ -63,8 +61,7 @@ function test_loadAndCheckOptionsFromFile()
   % makes sure that it is read correctly from
   opt = loadAndCheckOptions(filename);
 
-  expectedOptions = defaultOptions();
-  expectedOptions.taskName = 'vismotion';
+  expectedOptions = defaultOptions('vismotion');
   expectedOptions.space = 'individual';
 
   assertEqual(opt, expectedOptions);
@@ -105,8 +102,7 @@ function test_loadAndCheckOptionsFromSeveralFiles()
   % makes sure that the right json is read
   opt = loadAndCheckOptions();
 
-  expectedOptions = defaultOptions();
-  expectedOptions.taskName = 'vismotion';
+  expectedOptions = defaultOptions('vismotion');
   expectedOptions.space = 'individual';
   expectedOptions.funcVoxelDims = [1 1 1]';
 
diff --git a/tests/test_setBatchCoregistrationFuncToAnat.m b/tests/test_setBatchCoregistrationFuncToAnat.m
index 20c163eb..45589a53 100644
--- a/tests/test_setBatchCoregistrationFuncToAnat.m
+++ b/tests/test_setBatchCoregistrationFuncToAnat.m
@@ -16,7 +16,6 @@ function test_setBatchCoregistrationFuncToAnatBasic()
   subLabel = '02';
 
   opt = setOptions('vismotion', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
@@ -52,9 +51,7 @@ function test_setBatchCoregistrationFuncToAnatNoUnwarp()
   subLabel = '02';
 
   opt = setOptions('vismotion', subLabel);
-  opt = checkOptions(opt);
   opt.realign.useUnwarp = false;
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
diff --git a/tests/test_setBatchFactorialDesign.m b/tests/test_setBatchFactorialDesign.m
index 51186390..7be5aff5 100644
--- a/tests/test_setBatchFactorialDesign.m
+++ b/tests/test_setBatchFactorialDesign.m
@@ -16,8 +16,6 @@ function test_setBatchFactorialDesignBasic()
   opt = setOptions('vismotion');
   opt.subjects = {'01' '02'};
 
-  opt = checkOptions(opt);
-
   matlabbatch = [];
   matlabbatch = setBatchFactorialDesign(matlabbatch, opt, funcFWHM, conFWHM);
 
diff --git a/tests/test_setBatchMeanAnatAndMask.m b/tests/test_setBatchMeanAnatAndMask.m
index 6ff60d18..af30e028 100644
--- a/tests/test_setBatchMeanAnatAndMask.m
+++ b/tests/test_setBatchMeanAnatAndMask.m
@@ -15,9 +15,6 @@ function test_setBatchMeanAnatAndMaskBasic()
   opt = setOptions('vismotion');
   opt.subjects = {'01', '02'};
 
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
-
   matlabbatch = [];
   matlabbatch = setBatchMeanAnatAndMask(matlabbatch, opt, funcFWHM, pwd);
 
@@ -40,11 +37,11 @@ function test_setBatchMeanAnatAndMaskBasic()
   expectedBatch{1}.spm.util.imcalc = imcalc;
 
   %
-  imcalc.input{1, 1} = fullfile(opt.derivativesDir, 'sub-01', ...
+  imcalc.input{1, 1} = fullfile(opt.dir.stats, 'sub-01', ...
                                 'stats', ...
                                 'task-vismotion_space-MNI_FWHM-6', ...
                                 'mask.nii');
-  imcalc.input{2, 1} = fullfile(opt.derivativesDir, ...
+  imcalc.input{2, 1} = fullfile(opt.dir.stats, ...
                                 'sub-02', ...
                                 'stats', ...
                                 'task-vismotion_space-MNI_FWHM-6', ...
diff --git a/tests/test_setBatchRealign.m b/tests/test_setBatchRealign.m
index abccf14b..7ead8b76 100644
--- a/tests/test_setBatchRealign.m
+++ b/tests/test_setBatchRealign.m
@@ -19,7 +19,6 @@ function test_setBatchRealignBasic()
   subLabel = '01';
 
   opt = setOptions('MoAE', subLabel);
-  opt = checkOptions(opt);
   [BIDS, opt] = getData(opt);
 
   matlabbatch = [];
diff --git a/tests/test_setBatchSTC.m b/tests/test_setBatchSTC.m
index 28e9ace6..39435854 100644
--- a/tests/test_setBatchSTC.m
+++ b/tests/test_setBatchSTC.m
@@ -13,8 +13,6 @@ function test_setBatchSTCEmpty()
   subLabel = '02';
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
@@ -31,7 +29,6 @@ function test_setBatchSTCForce()
   subLabel = '02';
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = setDerivativesDir(opt);
 
   % we give it some slice timing value to force slice timing to happen
   opt.sliceOrder = linspace(0, 1.6, 10);
@@ -68,9 +65,7 @@ function test_setBatchSTCBasic()
   subLabel = '02';
 
   opt = setOptions('vismotion', subLabel);
-  opt = setDerivativesDir(opt);
   opt.query = struct('acq', '');
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
@@ -110,14 +105,11 @@ function test_setBatchSTCErrorInvalidInputTime()
   subLabel = '02';
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = setDerivativesDir(opt);
 
   opt.sliceOrder = linspace(0, 1.6, 10);
   opt.sliceOrder(end) = [];
   opt.STC_referenceSlice = 2; % impossible reference value
 
-  opt = checkOptions(opt);
-
   [BIDS, opt] = getData(opt);
 
   matlabbatch = [];
diff --git a/tests/test_setBatchSaveCoregistrationMatrix.m b/tests/test_setBatchSaveCoregistrationMatrix.m
index 582c346f..9492e226 100644
--- a/tests/test_setBatchSaveCoregistrationMatrix.m
+++ b/tests/test_setBatchSaveCoregistrationMatrix.m
@@ -16,9 +16,7 @@ function test_setBatchSaveCoregistrationMatrixBasic()
   subLabel = '02';
 
   opt = setOptions('vismotion', subLabel);
-  opt = setDerivativesDir(opt);
   opt.query = struct('acq', '');
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
diff --git a/tests/test_setBatchSelectAnat.m b/tests/test_setBatchSelectAnat.m
index 38023a7c..7edda8c1 100644
--- a/tests/test_setBatchSelectAnat.m
+++ b/tests/test_setBatchSelectAnat.m
@@ -17,7 +17,6 @@ function test_setBatchSelectAnatBasic()
   subLabel = '01';
 
   opt = setOptions('MoAE', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
diff --git a/tests/test_setBatchSkullStripping.m b/tests/test_setBatchSkullStripping.m
index f6f88159..788e0875 100644
--- a/tests/test_setBatchSkullStripping.m
+++ b/tests/test_setBatchSkullStripping.m
@@ -13,7 +13,6 @@ function test_setBatchSkullStrippingBasic()
   subLabel = '01';
 
   opt = setOptions('vislocalizer', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
diff --git a/tests/test_setBatchSmoothConImages.m b/tests/test_setBatchSmoothConImages.m
index 1c2dbd29..7a3364c9 100644
--- a/tests/test_setBatchSmoothConImages.m
+++ b/tests/test_setBatchSmoothConImages.m
@@ -15,7 +15,6 @@ function test_setBatchSmoothConImagesBasic()
 
   opt = setOptions('vismotion');
   opt.subjects = {'01', '02'};
-  opt = checkOptions(opt);
 
   [~, opt] = getData(opt);
 
@@ -24,16 +23,16 @@ function test_setBatchSmoothConImagesBasic()
 
   expectedBatch{1}.spm.spatial.smooth.fwhm = [6 6 6];
   expectedBatch{1}.spm.spatial.smooth.prefix = 's6';
-  expectedBatch{1}.spm.spatial.smooth.data = {fullfile(opt.derivativesDir, 'sub-01', 'stats', ...
+  expectedBatch{1}.spm.spatial.smooth.data = {fullfile(opt.dir.stats, 'sub-01', 'stats', ...
                                                        'task-vismotion_space-MNI_FWHM-6', ...
                                                        'con_0001.nii'); ...
-                                              fullfile(opt.derivativesDir, 'sub-01', 'stats', ...
+                                              fullfile(opt.dir.stats, 'sub-01', 'stats', ...
                                                        'task-vismotion_space-MNI_FWHM-6', ...
                                                        'con_0002.nii'); ...
-                                              fullfile(opt.derivativesDir, 'sub-01', 'stats', ...
+                                              fullfile(opt.dir.stats, 'sub-01', 'stats', ...
                                                        'task-vismotion_space-MNI_FWHM-6', ...
                                                        'con_0003.nii'); ...
-                                              fullfile(opt.derivativesDir, 'sub-01', 'stats', ...
+                                              fullfile(opt.dir.stats, 'sub-01', 'stats', ...
                                                        'task-vismotion_space-MNI_FWHM-6', ...
                                                        'con_0004.nii')};
   expectedBatch{1}.spm.spatial.smooth.dtype = 0;
@@ -41,16 +40,16 @@ function test_setBatchSmoothConImagesBasic()
 
   expectedBatch{2}.spm.spatial.smooth.fwhm = [6 6 6];
   expectedBatch{2}.spm.spatial.smooth.prefix = 's6';
-  expectedBatch{2}.spm.spatial.smooth.data = {fullfile(opt.derivativesDir, 'sub-02', 'stats', ...
+  expectedBatch{2}.spm.spatial.smooth.data = {fullfile(opt.dir.stats, 'sub-02', 'stats', ...
                                                        'task-vismotion_space-MNI_FWHM-6', ...
                                                        'con_0001.nii'); ...
-                                              fullfile(opt.derivativesDir, 'sub-02', 'stats', ...
+                                              fullfile(opt.dir.stats, 'sub-02', 'stats', ...
                                                        'task-vismotion_space-MNI_FWHM-6', ...
                                                        'con_0002.nii'); ...
-                                              fullfile(opt.derivativesDir, 'sub-02', 'stats', ...
+                                              fullfile(opt.dir.stats, 'sub-02', 'stats', ...
                                                        'task-vismotion_space-MNI_FWHM-6', ...
                                                        'con_0003.nii'); ...
-                                              fullfile(opt.derivativesDir, 'sub-02', 'stats', ...
+                                              fullfile(opt.dir.stats, 'sub-02', 'stats', ...
                                                        'task-vismotion_space-MNI_FWHM-6', ...
                                                        'con_0004.nii')};
   expectedBatch{2}.spm.spatial.smooth.dtype = 0;
diff --git a/tests/test_setBatchSmoothingFunc.m b/tests/test_setBatchSmoothingFunc.m
index 66b6f60f..de198f1d 100644
--- a/tests/test_setBatchSmoothingFunc.m
+++ b/tests/test_setBatchSmoothingFunc.m
@@ -18,7 +18,6 @@ function test_setBatchSmoothingFuncBasic()
   funcFWHM = 6;
 
   opt = setOptions('MoAE', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
diff --git a/tests/test_setBatchSubjectLevelContrasts.m b/tests/test_setBatchSubjectLevelContrasts.m
index b7958221..7995a8ab 100644
--- a/tests/test_setBatchSubjectLevelContrasts.m
+++ b/tests/test_setBatchSubjectLevelContrasts.m
@@ -14,14 +14,12 @@ function test_setBatchSubjectLevelContrastsBasic()
   funcFWHM = 6;
 
   opt = setOptions('vismotion', subLabel);
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   matlabbatch = [];
   matlabbatch = setBatchSubjectLevelContrasts(matlabbatch, opt, subLabel, funcFWHM);
 
   expectedBatch = [];
-  expectedBatch{end + 1}.spm.stats.con.spmmat = {fullfile(opt.derivativesDir, ...
+  expectedBatch{end + 1}.spm.stats.con.spmmat = {fullfile(opt.dir.stats, ...
                                                           'sub-01', ...
                                                           'stats', ...
                                                           'task-vismotion_space-MNI_FWHM-6', ...
diff --git a/tests/test_setBatchSubjectLevelGLMSpec.m b/tests/test_setBatchSubjectLevelGLMSpec.m
index ec2305f0..410a9599 100644
--- a/tests/test_setBatchSubjectLevelGLMSpec.m
+++ b/tests/test_setBatchSubjectLevelGLMSpec.m
@@ -17,8 +17,6 @@ function test_setBatchSubjectLevelGLMSpecBasic()
 
   opt = setOptions('MoAE', subLabel);
 
-  opt = checkOptions(opt);
-
   bidsCopyRawFolder(opt, 1);
 
   [BIDS, opt] = getData(opt);
diff --git a/tests/test_setBatchSubjectLevelResults.m b/tests/test_setBatchSubjectLevelResults.m
index ce34aae6..b8f4d636 100644
--- a/tests/test_setBatchSubjectLevelResults.m
+++ b/tests/test_setBatchSubjectLevelResults.m
@@ -18,8 +18,6 @@ function test_setBatchSubjectLevelResultsBasic()
 
   opt = setOptions('vismotion', subLabel);
   opt.space = 'MNI';
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   opt.result.Steps.Contrasts.Name = 'VisMot';
 
@@ -28,7 +26,7 @@ function test_setBatchSubjectLevelResultsBasic()
 
   expectedBatch = {};
 
-  expectedBatch{end + 1}.spm.stats.results.spmmat = {fullfile(opt.derivativesDir, ...
+  expectedBatch{end + 1}.spm.stats.results.spmmat = {fullfile(opt.dir.stats, ...
                                                               'sub-01', ...
                                                               'stats', ...
                                                               'task-vismotion_space-MNI_FWHM-6', ...
@@ -60,8 +58,6 @@ function test_setBatchSubjectLevelResultsErrorMissingContrastName()
 
   opt = setOptions('vismotion', subLabel);
   opt.space = 'MNI';
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   matlabbatch = [];
   assertExceptionThrown( ...
@@ -88,8 +84,6 @@ function test_setBatchSubjectLevelResultsErrorNoMAtchingContrast()
 
   opt = setOptions('vismotion', subLabel);
   opt.space = 'MNI';
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   opt.result.Steps.Contrasts.Name = 'NotAContrast';
 
diff --git a/tests/test_unit_createDataDictionary.m b/tests/test_unit_createDataDictionary.m
index 64aebba5..ba1aeecf 100644
--- a/tests/test_unit_createDataDictionary.m
+++ b/tests/test_unit_createDataDictionary.m
@@ -16,8 +16,6 @@ function test_createDataDictionaryBasic()
 
   opt = setOptions('vislocalizer', subLabel);
 
-  opt = checkOptions(opt);
-
   [BIDS, opt] = getData(opt);
 
   opt.query = struct('acq', '');
diff --git a/tests/test_unit_getInfo.m b/tests/test_unit_getInfo.m
index 8496f3e3..ec5198ca 100644
--- a/tests/test_unit_getInfo.m
+++ b/tests/test_unit_getInfo.m
@@ -13,7 +13,6 @@ function test_getInfoBasic()
   subLabel = 'ctrl01';
 
   opt = setOptions('vismotion', subLabel);
-  opt = checkOptions(opt);
 
   info = 'sessions';
 
@@ -55,7 +54,6 @@ function test_getInfoQuery()
   info = 'filename';
 
   opt = setOptions('vismotion', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
@@ -100,7 +98,6 @@ function test_getInfoQueryWithSessionRestriction()
   subLabel = 'ctrl01';
 
   opt = setOptions('vismotion', subLabel);
-  opt = checkOptions(opt);
 
   [BIDS, opt] = getData(opt);
 
diff --git a/tests/test_unit_getSliceOrder.m b/tests/test_unit_getSliceOrder.m
index 12f55d2a..379e0ab1 100644
--- a/tests/test_unit_getSliceOrder.m
+++ b/tests/test_unit_getSliceOrder.m
@@ -11,7 +11,6 @@
 function test_getSliceOrderBasic()
 
   opt = setOptions('vismotion');
-  opt = checkOptions(opt);
 
   [~, opt] = getData(opt);
   BIDS_sliceOrder = getSliceOrder(opt, 0);
@@ -40,7 +39,6 @@ function test_getSliceOrderBasic()
 function test_getSliceOrderEmpty()
 
   opt = setOptions('vislocalizer');
-  opt = checkOptions(opt);
 
   [~, opt] = getData(opt);
 
@@ -55,7 +53,6 @@ function test_getSliceOrderFromOptions()
   opt = setOptions('vislocalizer');
   opt.STC_referenceSlice = 1000;
   opt.sliceOrder = 0:250:2000;
-  opt = checkOptions(opt);
 
   [~, opt] = getData(opt);
   BIDS_sliceOrder = getSliceOrder(opt, 0);
diff --git a/tests/test_unit_getSubjectList.m b/tests/test_unit_getSubjectList.m
index 4d4a6e5b..880c1d89 100644
--- a/tests/test_unit_getSubjectList.m
+++ b/tests/test_unit_getSubjectList.m
@@ -11,8 +11,6 @@
 function test_getSubjectListNone()
 
   opt = setOptions('vismotion');
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   BIDS = bids.layout(opt.derivativesDir);
 
@@ -27,8 +25,6 @@ function test_getSubjectListNone()
 function test_getSubjectListGroup()
 
   opt = setOptions('vismotion');
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   BIDS = bids.layout(opt.derivativesDir);
 
@@ -46,8 +42,6 @@ function test_getSubjectListGroup()
 function test_getSubjectListBasic()
 
   opt = setOptions('vismotion');
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   BIDS = bids.layout(opt.derivativesDir);
 
@@ -64,8 +58,6 @@ function test_getSubjectListBasic()
 function test_getSubjectListErrorSubject()
 
   opt = setOptions('vismotion', '03');
-  opt = setDerivativesDir(opt);
-  opt = checkOptions(opt);
 
   BIDS = bids.layout(opt.derivativesDir);
 
diff --git a/tests/test_unit_specifyContrasts.m b/tests/test_unit_specifyContrasts.m
index 56cae880..373a13c5 100644
--- a/tests/test_unit_specifyContrasts.m
+++ b/tests/test_unit_specifyContrasts.m
@@ -15,8 +15,6 @@ function test_specifyContrastsBasic()
   funcFWFM = 6;
 
   opt = setOptions('vismotion', subLabel);
-  opt = checkOptions(opt);
-  opt = setDerivativesDir(opt);
 
   ffxDir = getFFXdir(subLabel, funcFWFM, opt);
 
diff --git a/tests/utils/defaultOptions.m b/tests/utils/defaultOptions.m
index 3337b905..5c7211f8 100644
--- a/tests/utils/defaultOptions.m
+++ b/tests/utils/defaultOptions.m
@@ -1,12 +1,14 @@
 % (C) Copyright 2021 CPP BIDS SPM-pipeline developers
 
-function expectedOptions = defaultOptions()
+function expectedOptions = defaultOptions(taskName)
 
   expectedOptions.sliceOrder = [];
   expectedOptions.STC_referenceSlice = [];
 
   expectedOptions.dataDir = '';
   expectedOptions.derivativesDir = '';
+  expectedOptions.dir = struct('raw', '', ...
+                               'derivatives', '');
 
   expectedOptions.funcVoxelDims = [];
 
@@ -31,7 +33,8 @@
 
   expectedOptions.contrastList = {};
 
-  expectedOptions.glmQA.do = true;
+  expectedOptions.glm.QA.do = true;
+  expectedOptions.glm.roibased.do = false;
 
   expectedOptions.model.file = '';
   expectedOptions.model.hrfDerivatives = [0 0];
@@ -42,6 +45,12 @@
   expectedOptions.parallelize.nbWorkers = 3;
   expectedOptions.parallelize.killOnExit = true;
 
+  if nargin > 0
+    expectedOptions.taskName = taskName;
+  end
+
   expectedOptions = orderfields(expectedOptions);
 
+  expectedOptions = setStatsDir(expectedOptions);
+
 end
diff --git a/tests/utils/setOptions.m b/tests/utils/setOptions.m
index 27a05a8b..9e12acb8 100644
--- a/tests/utils/setOptions.m
+++ b/tests/utils/setOptions.m
@@ -4,6 +4,8 @@
 
   thisDir = fileparts(mfilename('fullpath'));
 
+  opt.dir = [];
+
   if strcmp(task, 'MoAE')
 
     opt.dataDir = fullfile(thisDir, ...
@@ -22,6 +24,8 @@
 
   end
 
+  opt = checkOptions(opt);
+
   if nargin > 1
     opt.subjects = {subLabel};
   end