diff --git a/.github/workflows/miss_hit.cfg b/.github/workflows/miss_hit.cfg
new file mode 100644
index 0000000..d02fa5c
--- /dev/null
+++ b/.github/workflows/miss_hit.cfg
@@ -0,0 +1,23 @@
+# miss_hit configuration
+# for matlab linting and static analysis
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+
+project_root
+
+octave: false
+
+line_length: 100
+
+suppress_rule: "copyright_notice"
+
+tab_width: 2
+
+# snake_case
+regex_script_name: "[a-zA-Z]+(_[a-zA-Z0-9]*)*"
+regex_function_name: "[a-zA-Z]+(_[a-zA-Z0-9]*)*"
+
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 10
+metric "parameters": limit 5
diff --git a/.github/workflows/run_demos_ci.m b/.github/workflows/run_demos_ci.m
new file mode 100644
index 0000000..704836c
--- /dev/null
+++ b/.github/workflows/run_demos_ci.m
@@ -0,0 +1,22 @@
+% run demos with moxunit in github CI
+
+root_dir = getenv('GITHUB_WORKSPACE');
+
+% MOxUnit and MOcov need to be in the matlab path
+addpath(fullfile(root_dir, 'MOcov', 'MOcov'));
+cd(fullfile(root_dir, 'MOxUnit', 'MOxUnit'));
+run moxunit_set_path();
+
+% add glm single to path
+cd(root_dir);
+setup();
+
+this_folder = fileparts(mfilename('fullpath'));
+test_folder = this_folder;
+success = moxunit_runtests(test_folder, '-verbose', '-recursive');
+
+if success
+  system('echo 0 > test_report.log');
+else
+  system('echo 1 > test_report.log');
+end
diff --git a/.github/workflows/run_demos_matlab.yaml b/.github/workflows/run_demos_matlab.yaml
new file mode 100644
index 0000000..7aa9ee3
--- /dev/null
+++ b/.github/workflows/run_demos_matlab.yaml
@@ -0,0 +1,54 @@
+name: MATLAB demos
+
+# Uses the cron schedule for github actions
+#
+#   will run at 00H00 run on the 1 and 15 of every month
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+#         ┌───────────── minute (0 - 59)
+#         │ ┌───────────── hour (0 - 23)
+#         │ │ ┌───────────── day of the month (1 - 31)
+#         │ │ │    ┌───────────── month (1 - 12 or JAN-DEC): * means all
+#         │ │ │    │ ┌───────────── day of the week (0 - 6 or SUN-SAT): * means all
+#         │ │ │    │ │
+#         │ │ │    │ │
+#         │ │ │    │ │
+# 
+# - cron "0 0 1,15 * *"
+
+on:
+  schedule:
+    - cron: "0 0 1,15 * *"
+
+jobs:
+  demos:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - name: Install MATLAB
+        uses: matlab-actions/setup-matlab@v1.0.1
+        with:
+          release: R2020a
+
+      - name: Shallow clone GLMsingle
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 0 # 0 means we only get the last commit, not the whole git history
+
+      - name: Install Moxunit and MOcov
+        run: |
+          git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
+          git clone https://github.com/MOcov/MOcov.git --depth 1
+
+      - name: Run commands
+        uses: matlab-actions/run-command@v1.0.1
+        with:
+          command:
+              cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows'));
+              run run_demos_ci;
+
+      - name: Check logs
+        run: |
+          cat test_report.log | grep 0
\ No newline at end of file
diff --git a/.github/workflows/run_tests_ci.m b/.github/workflows/run_tests_ci.m
new file mode 100644
index 0000000..ecf8798
--- /dev/null
+++ b/.github/workflows/run_tests_ci.m
@@ -0,0 +1,11 @@
+% run tests with code coverage via the run_tests scripts in the root folder.
+
+root_dir = getenv('GITHUB_WORKSPACE');
+
+% MOxUnit and MOcov need to be in the matlab path
+addpath(fullfile(root_dir, 'MOcov', 'MOcov'));
+cd(fullfile(root_dir, 'MOxUnit', 'MOxUnit'));
+run moxunit_set_path();
+
+cd(root_dir);
+run run_tests();
diff --git a/.github/workflows/run_tests_matlab.yaml b/.github/workflows/run_tests_matlab.yaml
new file mode 100644
index 0000000..544ad9f
--- /dev/null
+++ b/.github/workflows/run_tests_matlab.yaml
@@ -0,0 +1,68 @@
+name: MATLAB tests
+
+# Installs
+# - MATLAB github action
+# - MOXunit
+# - MOcov
+# Get test data
+# cd into .github/workflows
+# run .github/workflows/tests_matlab.m
+# If tests pass, uploads coverage to codecov
+
+on:
+  push:
+    # TODO only run on master branch on push 
+    branches: ["main"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+  tests:
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest] # "macos-latest" or "windows-latest" don't work (yet?)
+        matlab-version: ["R2020a"] # add more versions if needed: "R2021a"
+      fail-fast: false  # Don't cancel all jobs if one fails
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Install MATLAB ${{ matrix.matlab-version }}
+        uses: matlab-actions/setup-matlab@v1.0.1
+        with:
+          release: ${{ matrix.matlab-version }}
+
+      - name: Shallow clone GLMsingle
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 0 # 0 means we only get the last commit, not the whole git history
+
+      - name: Install Moxunit and MOcov
+        run: |
+          git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
+          git clone https://github.com/MOcov/MOcov.git --depth 1
+
+      - name: Download data
+        run: make tests/data/nsdcoreexampledataset.mat
+
+      - name: Run tests
+        uses: matlab-actions/run-command@v1.0.1
+        with:
+          command:
+            cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows'));
+            run run_tests_ci;
+
+      - name: Check logs
+        run: |
+          cat test_report.log | grep 0
+          bash <(curl -s https://codecov.io/bash)
+
+      - name: Code coverage
+        uses: codecov/codecov-action@v1
+        with:
+          file: coverage.xml # optional
+          flags: matlab # optional
+          name: codecov-umbrella # optional
+          fail_ci_if_error: true # optional (default = false)
diff --git a/.github/workflows/test_demos.m b/.github/workflows/test_demos.m
new file mode 100644
index 0000000..64e73ba
--- /dev/null
+++ b/.github/workflows/test_demos.m
@@ -0,0 +1,32 @@
+function test_suite = test_demos %#ok<*STOUT>
+
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+
+  initTestSuite;
+
+end
+
+function test_demo1()
+
+  run(fullfile(root_dir(), 'matlab', 'examples', 'example1'));
+
+end
+
+function test_demo2()
+
+  run(fullfile(root_dir(), 'matlab', 'examples', 'example2'));
+
+end
+
+function value = root_dir()
+
+  value = getenv('GITHUB_WORKSPACE');
+
+  if isempty(value)
+    value =  fullfile(fileparts(mfilename('fullpath')), '..', '..');
+  end
+
+end
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index baaa794..94480c4 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -2,16 +2,34 @@
 
 Information for anyone who would like to contribute to this repository.
 
+- [CONTRIBUTING](#contributing)
+  - [Repository map](#repository-map)
+  - [Generic](#generic)
+    - [Makefile](#makefile)
+    - [pre-commit](#pre-commit)
+  - [Matlab](#matlab)
+    - [Style guide](#style-guide)
+    - [Tests](#tests)
+      - [Adding new tests](#adding-new-tests)
+    - [Continuous integration](#continuous-integration)
+      - [Tests](#tests-1)
+      - [Demos](#demos)
+  - [Python](#python)
+    - [Style guide](#style-guide-1)
+    - [Tests](#tests-2)
+      - [Demos](#demos-1)
+    - [Continuous integration](#continuous-integration-1)
+
 ## Repository map
 
 ```bash
 ├── .git
 ├── .github
 │   └── workflows         # Github continuous integration set up
-├── examples
+├── examples              # Python demos
 │   ├── data
 │   ├── example1outputs
-│   ├── example2outputs
+│   └── example2outputs
 ├── glmsingle             # Python implementation
 │   ├── cod
 │   ├── design
@@ -21,11 +39,13 @@ Information for anyone who would like to contribute to this repository.
 │   ├── ssq
 │   └── utils
 ├── matlab                # Matlab implementation
-│   ├── examples
-│   ├── fracridge
+│   ├── examples          # Matlab demos
+│   ├── fracridge         # Fracridge submodule
 │   └── utilities
 └── tests                 # Python and Matlab tests
-    └── data
+    ├── data              # Data used as inputs for the tests
+    └── expected          # Expected results of the tests
+│       └── matlab
 
 ```
 
@@ -33,18 +53,188 @@ Information for anyone who would like to contribute to this repository.
 
 ### Makefile
 
+A `Makefile` is used to help set / and automate some things.
+
+In a terminal type `make help` to see what some of the different "recipes" you
+can run with this `Makefile`.
+
+See
+[here for a short intro on using `Makefiles`](https://the-turing-way.netlify.app/reproducible-research/make.html)
+
 ### pre-commit
 
+You can use the [`pre-commit` python package](https://pre-commit.com/) in this
+repo to make sure you only commit properly formatted files (for example `.yml`
+files).
+
+1. Install `pre-commit`
+
+```bash
+$ pip3 install pre-commit
+```
+
+It is also included in `requirements_dev.txt`, so it will installed by running:
+
+```bash
+$ pip3 install -r requirements_dev.txt
+```
+
+The `.pre-commit-config.yml` file defines the checks to run when committing
+files.
+
+1. Run the following command to install the `pre-commit` "hooks"
+
+```bash
+$ pre-commit install
+```
+
 ## Matlab
 
 ### Style guide
 
+The [`miss_hit` python package](https://misshit.org/) is used to help ensure a
+consistent coding style for some of the MATLAB code.
+
+`miss_hit` can check code style, do a certain amount of automatic code
+reformating and prevent the code complexity from getting out of hand by running
+static code analysis (Static analysis can is a way to measure and track software
+quality metrics without additional code like tests).
+
+`miss_hit` is quite configurable via the use of `miss_hit.cfg` files.
+
+Install `miss_hit`:
+
+```bash
+$ pip3 install miss_hit
+```
+
+It is also included in `requirements_dev.txt`, so it will installed by running:
+
+```bash
+$ pip3 install -r requirements_dev.txt
+```
+
+Style-check your program:
+
+```bash
+$ mh_style --fix path_to_folder_or_m_file
+```
+
+Make sure your code does not get too complex:
+
+```bash
+$ mh_metric --ci
+```
+
+You can rule several of those checks by simply typing
+
+```bash
+make lint/miss_hit
+```
+
 ### Tests
 
-#### Demos
+For an introduction to testing see
+[here](https://the-turing-way.netlify.app/reproducible-research/make.html).
+
+Running the tests require to have the following toolboxes in your MATLAB path:
+
+- the [MOxUnit testing framework](https://github.com/MOxUnit/MOxUnit) to run the
+  tests
+  ([see installation procedure](https://github.com/MOxUnit/MOxUnit#installation))
+- [MOcov](https://github.com/MOcov/MOcov)) to get a code coverage estimate
+  ([see installation procedure](https://github.com/MOcov/MOcov#installation))
+
+All the tests are in the `tests` folder in files starting with `test_*.m`.
+
+To Download the data required for running the tests (this data is common for
+MATLAB and python tests), type:
+
+```bash
+make tests/data/nsdcoreexampledataset.mat
+```
+
+Only some specific results are checked by the system tests: those can be found
+in `tests/expected/matlab`. See this [README](./tests/expected/matlab/README.md)
+for more information.
+
+To run **all** the tests and get code coverage, you can
+
+1. type the following in a terminal
+
+```
+make test-matlab
+```
+
+1. run `moxunit_runtests` in MATLAB to run all `test_*.m` files in in the
+   present working directory.
+
+1. run the `run_tests.m` in MATLAB
+
+You can also run all the tests contained in a specific `test_*.m` file directly,
+by running that file only.
+
+#### Adding new tests
+
+A typical MoxUnit test file starts with with `test_` and would look something
+like this.
+
+```matlab
+function test_suite=test_sum_of_squares
+
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite();
+
+end
+
+function test_sum_of_squares_basic
+
+    % given
+    a = 2;
+    b = 3;
+
+    % when
+    result = sum_of_squares([a, b])
+
+    % then
+    expected = 13;
+    assertEqual(result, expected);
+
+end
+
+% New tests can added as new sub functions
+
+```
 
 ### Continuous integration
 
+We use Github to run several workflows for continuous integration.
+
+#### Tests
+
+The matlab tests are run by the workflow:
+`.github/workflows/run_tests_matlab.yaml`. It sets up MATLAB, Moxunit and Mocov
+and then then calls `.github/workflows/run_tests_ci.m` to run the tests via
+`run_tests.m`.
+
+Those tests should be run with every push on the `master` branch and on pull
+request that target the `master` branch.
+
+#### Demos
+
+The demos in the `matlab/examples` folder are run automatically in Github CI at
+regular intervals.
+
+The matlab demos are run by the workflow:
+`.github/workflows/run_demos_matlab.yaml`. The demos are run by calling
+`.github/workflows/run_demos_ci.m` and also each demo is run via a MoxUnit test
+(see `.github/workflows/test_demos.m`) to make sure that if the first one
+crashes, then the second one will still be run (easier than setting up parallel
+jobs in CI).
+
 ## Python
 
 ### Style guide
@@ -53,4 +243,4 @@ Information for anyone who would like to contribute to this repository.
 
 #### Demos
 
-### Continuous integration
\ No newline at end of file
+### Continuous integration
diff --git a/Makefile b/Makefile
index 75e39ce..2e3a9ac 100644
--- a/Makefile
+++ b/Makefile
@@ -47,11 +47,11 @@ install_dev: ## install for both matlab and python developpers
 	pip install -e .
 	pip install -r requirements_dev.txt
 
-lint: lint/black lint/flake8 lint/miss_hit ## check style
+lint: lint/black lint/flake8 lint/miss_hit ## check style for MATLAB and python
 
-test: test-matlab test-python
+test: test-matlab test-python # run tests with MATLAB and python
 
-tests/data/nsdcoreexampledataset.mat: 
+tests/data/nsdcoreexampledataset.mat: ## install test data
 	mkdir tests/data
 	curl -fsSL --retry 5 -o "tests/data/nsdcoreexampledataset.mat" https://osf.io/k89b2/download
 
@@ -64,8 +64,9 @@ tests/data/nsdcoreexampledataset.mat:
 
 lint/miss_hit: ## lint and checks matlab code
 	mh_style --fix tests && mh_metric --ci tests && mh_lint tests
+	mh_style --fix .github/workflows && mh_metric --ci .github/workflows && mh_lint .github/workflows
 
-test-matlab: tests/data/nsdcoreexampledataset.mat
+test-matlab: tests/data/nsdcoreexampledataset.mat ## run tests with MATLAB
 	$(MATLAB) $(MATLAB_ARG) -r "run_tests; exit()"
 
 coverage-matlab: test-matlab
diff --git a/README.md b/README.md
index 336ed01..e6ba459 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,6 @@
+[![MATLAB test](https://github.com/cvnlab/GLMsingle/actions/workflows/run_tests_matlab.yml/badge.svg)](https://github.com/cvnlab/GLMsingle/actions/workflows/run_tests_matlab.yml)
+[![MATLAB demos](https://github.com/cvnlab/GLMsingle/actions/workflows/run_demos_matlab.yml/badge.svg)](https://github.com/cvnlab/GLMsingle/actions/workflows/run_demos_matlab.yml)
+
 # GLMsingle
 
 ![image](https://user-images.githubusercontent.com/35503086/151108958-24479034-c7f7-4734-b903-9046ba6a78ac.png)
diff --git a/run_tests.m b/run_tests.m
new file mode 100644
index 0000000..9ee5f41
--- /dev/null
+++ b/run_tests.m
@@ -0,0 +1,29 @@
+function run_tests()
+
+  % run tests with code coverage
+
+  tic;
+
+  cd(fileparts(mfilename('fullpath')));
+
+  fprintf('\nHome is %s\n', getenv('HOME'));
+
+  folder_to_cover = fullfile(pwd, 'matlab');
+
+  test_folder = fullfile(pwd, 'tests');
+
+  success = moxunit_runtests(test_folder, ...
+                             '-verbose', '-recursive', '-with_coverage', ...
+                             '-cover', folder_to_cover, ...
+                             '-cover_xml_file', 'coverage.xml', ...
+                             '-cover_html_dir', fullfile(pwd, 'coverage_html'));
+
+  if success
+    system('echo 0 > test_report.log');
+  else
+    system('echo 1 > test_report.log');
+  end
+
+  toc;
+
+end
diff --git a/tests/expected/matlab/README.md b/tests/expected/matlab/README.md
new file mode 100644
index 0000000..158f6a2
--- /dev/null
+++ b/tests/expected/matlab/README.md
@@ -0,0 +1,28 @@
+# Content
+
+Data used for the expected results of the system tests.
+
+```bash
+ ├── TYPEB_FITHRF.mat
+ ├── TYPEC_FITHRF_GLMDENOISE.mat
+ └── TYPED_FITHRF_GLMDENOISE_RR.mat
+```
+
+Contain the expected value for:
+
+- `HRFindex` values for `results{2:4}` for `tests/test_glmsingleunit.m`.
+
+`TYPED_FITHRF_GLMDENOISE_RR.mat` also contains `R2` values.
+
+Generated with MATLAB 2017a on Ubuntu 18.04.
+
+If new expected data needs to be generated, this can be done from the output of
+`tests/test_GLMestimatesingletrial.m` that will be saved in `tests/outputs`.
+
+Some basic sanity checks can be run on those data with
+`tests/expected/matlab/sanity_checks.m`
+
+- like making sure that the there is nothing "strange" in the range of R2 values
+  tested.
+
+![histogram_R2](./histogram_R2.png)
diff --git a/tests/expected/matlab/TYPEB_FITHRF.mat b/tests/expected/matlab/TYPEB_FITHRF.mat
new file mode 100644
index 0000000..2713bea
Binary files /dev/null and b/tests/expected/matlab/TYPEB_FITHRF.mat differ
diff --git a/tests/expected/matlab/TYPEC_FITHRF_GLMDENOISE.mat b/tests/expected/matlab/TYPEC_FITHRF_GLMDENOISE.mat
new file mode 100644
index 0000000..07ac64a
Binary files /dev/null and b/tests/expected/matlab/TYPEC_FITHRF_GLMDENOISE.mat differ
diff --git a/tests/expected/matlab/TYPED_FITHRF_GLMDENOISE_RR.mat b/tests/expected/matlab/TYPED_FITHRF_GLMDENOISE_RR.mat
new file mode 100644
index 0000000..8fe2298
Binary files /dev/null and b/tests/expected/matlab/TYPED_FITHRF_GLMDENOISE_RR.mat differ
diff --git a/tests/expected/matlab/histogram_R2.png b/tests/expected/matlab/histogram_R2.png
new file mode 100644
index 0000000..60dbe6f
Binary files /dev/null and b/tests/expected/matlab/histogram_R2.png differ
diff --git a/tests/expected/matlab/sanity_checks.m b/tests/expected/matlab/sanity_checks.m
new file mode 100644
index 0000000..f336865
--- /dev/null
+++ b/tests/expected/matlab/sanity_checks.m
@@ -0,0 +1,21 @@
+% make sure we have no NaN / Inf in our expected results
+% aslo plots a couple of figures for quick visual inspection
+
+clear
+clc
+close all
+
+load('TYPED_FITHRF_GLMDENOISE_RR.mat')
+
+assert(any(isnan(R2(:))) == 0);
+assert(any(isinf(R2(:))) == 0);
+
+figure('name', 'histogram R2')
+hist(R2(:), 100);
+print('histogram_R2.png', '-dpng');
+
+figure('name', 'R2')
+imagesc(R2, [0 100])
+
+figure('name', 'HRFindex')
+imagesc(HRFindex, [1 20])
\ No newline at end of file
diff --git a/tests/miss_hit.cfg b/tests/miss_hit.cfg
new file mode 100644
index 0000000..ca6e42d
--- /dev/null
+++ b/tests/miss_hit.cfg
@@ -0,0 +1,22 @@
+# miss_hit configuration
+# for matlab linting and static analysis
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+
+project_root
+
+octave: false
+
+line_length: 100
+
+suppress_rule: "copyright_notice"
+
+tab_width: 2
+
+# snake_case
+regex_function_name: "[a-zA-Z]+(_[a-zA-Z]*)*"
+
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 10
+metric "parameters": limit 5
diff --git a/tests/test_GLMestimatesingletrial.m b/tests/test_GLMestimatesingletrial.m
new file mode 100644
index 0000000..c42120b
--- /dev/null
+++ b/tests/test_GLMestimatesingletrial.m
@@ -0,0 +1,71 @@
+function test_suite = test_GLMestimatesingletrial %#ok<*STOUT>
+
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+
+  initTestSuite;
+
+end
+
+function test_GLMestimatesingletrial_system()
+
+  % "end-to-end" test of GLMestimatesingletrial
+  % only checks the HRF index of 400 voxels
+
+  [data, expected, output_dir] = set_up_test();
+
+  % GIVEN
+  design = data.design(1:3);
+  stimdur = data.stimdur;
+  tr = data.tr;
+  data = cellfun(@(x) x(51:70, 8:27, 1, :), data.data(1:3), 'UniformOutput', 0);
+
+  % WHEN
+  results = GLMestimatesingletrial(design, ...
+                                   data, ...
+                                   stimdur, ...
+                                   tr, ...
+                                   output_dir, ...
+                                   struct('wantmemoryoutputs', [1 1 1 1]));
+
+  % THEN
+  assertEqual(results{2}.HRFindex, expected{2}.HRFindex);
+  assertEqual(results{3}.HRFindex, expected{3}.HRFindex);
+  assertEqual(results{4}.HRFindex, expected{4}.HRFindex);
+
+  assertElementsAlmostEqual(results{4}.R2, expected{4}.R2, 'absolute', 1e-1);
+
+  clean_up();
+
+end
+
+function [data, expected, output_dir] = set_up_test()
+
+  test_dir = fileparts(mfilename('fullpath'));
+
+  data_dir = fullfile(test_dir, 'data');
+  data_file = fullfile(data_dir, 'nsdcoreexampledataset.mat');
+  data = load(data_file);
+
+  expected_dir = fullfile(test_dir, 'expected', 'matlab');
+  load(fullfile(expected_dir, 'TYPEB_FITHRF.mat'));
+  expected{2}.HRFindex = HRFindex;
+  load(fullfile(expected_dir, 'TYPEC_FITHRF_GLMDENOISE.mat'));
+  expected{3}.HRFindex = HRFindex;
+  load(fullfile(expected_dir, 'TYPED_FITHRF_GLMDENOISE_RR.mat'));
+  expected{4}.HRFindex = HRFindex;
+  expected{4}.R2 = R2;
+
+  output_dir = fullfile(test_dir, 'outputs', 'matlab');
+
+  run(fullfile(test_dir, '..', 'setup.m'));
+
+end
+
+function clean_up()
+
+  % ununsed for now
+
+end