diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 00000000..dfe07704
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto
diff --git a/.github/workflows/check_markdown.yml b/.github/workflows/check_markdown.yml
new file mode 100644
index 00000000..46725a09
--- /dev/null
+++ b/.github/workflows/check_markdown.yml
@@ -0,0 +1,34 @@
+name: Check Markdown
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - uses: actions/setup-node@v2
+      with:
+        node-version: '10'
+
+    - name: Install dependencies and check markdown
+      run: |
+        npm install `cat npm-requirements.txt`
+        npx remark README.md --frail  
+        npx remark ./notebooks/ --frail
+        npx remark ./tests/ --frail
+        npx remark ./docs/ --frail
+
+
diff --git a/.github/workflows/check_md_links.yml b/.github/workflows/check_md_links.yml
index c54aac1c..62bb95e1 100644
--- a/.github/workflows/check_md_links.yml
+++ b/.github/workflows/check_md_links.yml
@@ -6,7 +6,6 @@ on:
   push:
     branches:
       - master
-      - dev
   pull_request:
     branches: '*'
 
diff --git a/.github/workflows/miss_hit.yml b/.github/workflows/miss_hit.yml
index d4cb7ae8..5c5e561d 100644
--- a/.github/workflows/miss_hit.yml
+++ b/.github/workflows/miss_hit.yml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - dev
   pull_request:
     branches: '*'
 
@@ -28,12 +27,16 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip3 install install miss_hit
+        pip3 install -r requirements.txt
 
-    - name: Miss_hit code quality
+    - name: MISS_HIT Code style
       run: |
-        mh_metric . --ci
+        mh_style --process-slx
 
-    - name: Miss_hit code style
+    - name: MISS_HIT Metrics
       run: |
-        mh_style .
+        mh_metric --ci
+
+    - name: MISS_HIT Bug finder
+      run: |
+        mh_lint
diff --git a/.github/workflows/moxunit.yml b/.github/workflows/moxunit.yml
index 16a9ee9c..0063a04c 100644
--- a/.github/workflows/moxunit.yml
+++ b/.github/workflows/moxunit.yml
@@ -1,9 +1,10 @@
-name: CI
+name: MOxUnit
 
 on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches: '*'
 
@@ -11,10 +12,21 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
+
     - uses: actions/checkout@v2
       with:
         submodules: true
         fetch-depth: 1
+
+    - name: Make jsonread for octave
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get -y install octave 
+        sudo apt-get -y install liboctave-dev
+        cd lib/JSONio
+        mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
+      # cd ../..
+
     - name: MOxUnit Action
       uses: joergbrech/moxunit-action@v1.1
       with:
@@ -22,6 +34,7 @@ jobs:
         src: src
         with_coverage: true
         cover_xml_file: coverage.xml
+
     - name: Code coverage
       uses: codecov/codecov-action@v1
       with:
diff --git a/.gitignore b/.gitignore
index 3a9f5620..c1db3745 100644
--- a/.gitignore
+++ b/.gitignore
@@ -23,8 +23,20 @@ tests/*.tsv*
 check_my_code_report.txt
 
 # jupyter notebook checkpoints
-.ipynb_checkpoints
-*/.ipynb_checkpoints/*
+notebooks/.ipynb_checkpoints/*
+notebooks/source/*
+notebooks/output/*
+notebooks/new_experiment/*
 
+# ignore node js files
+node_modules/*
+package-lock.json
 
+# visual studio code stuff
+.vscode
 
+# virtual env
+cpp_bids/*
+
+# documentation
+docs/build/*
diff --git a/.readthedocs.yml b/.readthedocs.yml
new file mode 100644
index 00000000..ec0951f4
--- /dev/null
+++ b/.readthedocs.yml
@@ -0,0 +1,26 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  builder: html
+  fail_on_warning: true
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: requirements.txt
\ No newline at end of file
diff --git a/.travis.yml b/.travis.yml
index d5cfa910..87c8f835 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,17 +3,12 @@
 # have set it up to run continuous integration on this this repo
 
 # Linux distribution (bionic beaver)
-dist: bionic
+dist: focal
 
 # Language and version
 language: node_js
 node_js:
-  - "10"
-
-cache:
-  apt: true # only works with Pro version
-  directories:
-  - node_modules # NPM packages for the remark markdown linter
+  - "11"
 
 branches:
   only:  # only run the CI for those branches 
@@ -33,7 +28,7 @@ before_install:
   - travis_retry sudo apt-get -y install nodejs
   - travis_retry sudo apt-get -y install npm
   # Install BIDS-Validator
-  - sudo npm install -g bids-validator@1.5.4
+  - sudo npm install -g bids-validator@1.5.7
 
 install:
   # make octave file the JSONio submodule
@@ -51,12 +46,3 @@ jobs:
 
     - name: "BIDS validator: create and check dataset"
       script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders
-
-    - name: "Check markdown"
-      before_script:
-        - npm install `cat npm-requirements.txt`
-      script:
-        - remark README.md --frail
-        - remark ./notebooks/ --frail
-        - remark ./tests/ --frail
-        - remark ./docs/ --frail
diff --git a/.zenodo.json b/.zenodo.json
new file mode 100644
index 00000000..6edf043c
--- /dev/null
+++ b/.zenodo.json
@@ -0,0 +1,35 @@
+{
+  "title": "CPP_BIDS",
+  "description": "A lightweight Octave/MATLAB toolbox to help create BIDS data sets from source.",
+  "creators": [
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Gau, Rémi",
+      "orcid": "0000-0002-1535-9767"
+    },
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Barilari, Marco",
+      "orcid": "0000-0002-3313-3120"
+    },
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Battal, Ceren",
+      "orcid": "0000-0002-9844-7630"
+    },
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Lenc, Thomas",
+      "orcid": "0000-0001-5796-1388"
+    }
+  ],
+  "keywords": [
+    "BIDS",
+    "brain imaging data structure",
+    "neuroscience",
+    "MATLAB",
+    "Octave"
+  ],
+  "license": "MIT license",
+  "upload_type": "software"
+}
\ No newline at end of file
diff --git a/README.md b/README.md
index 1d1e474e..6fb0f241 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,14 @@
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/CPP_BIDS/master?filepath=notebooks%2Fbasic_usage.ipynb)
 
+**Documentation**
+
+[![Documentation Status: stable](https://readthedocs.org/projects/cpp-bids/badge/?version=stable)](https://cpp-bids.readthedocs.io/en/stable/?badge=stable)
+
+**Cite it**
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4007674.svg)](https://doi.org/10.5281/zenodo.4007674)
+
 **Unit tests and coverage**
 
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_BIDS/actions)
@@ -19,7 +27,7 @@
 
 [![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
 
-* * *
+---
 
 # CPP_BIDS
 
@@ -44,42 +52,24 @@ A set of function for matlab and octave to create
 structure and filenames for the output of behavioral, EEG, fMRI, eyetracking
 studies.
 
-## Output format
-
-### Modality agnostic aspect
-
-Subjects, session and run number labels will be numbers with zero padding up to
-3 values (e.g subject 1 will become `sub-001`).
-
-A session folder will ALWAYS be created even if not requested (default will be
-`ses-001`).
-
-Task labels will be printed in camelCase in the filenames.
-
-Time stamps are added directly in the filename by adding a suffix
-`_date-YYYYMMDDHHMM` which makes the file name non-BIDS compliant. This was
-added to prevent overwriting files in case a certain run needs to be done a
-second time because of a crash (Some of us are paranoid about keeping even
-cancelled runs during my experiments). This suffix should be removed to make the
-data set BIDS compliant. See `convertSourceToRaw.m` for more details.
-
-For example:
-
-```bash
-sub-090/ses-003/sub-090_ses-003_task-auditoryTask_run-023_events_date-202007291536.tsv
-```
-
 ## Documentation
 
 -   [Installation](./docs/installation.md)
 -   [How to use it: jupyter notebooks](./notebooks)
--   [Functions description](./docs/functions-description.md)
+-   [General documentation](https://cpp-bids.readthedocs.io/en/dev/index.html)
 
 ## Contributing
 
 Feel free to open issues to report a bug and ask for improvements.
 
-### Guidestyle
+If you want to contribute, have a look at our
+[contributing guidelines](https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md)
+that are meant to guide you and help you get started. If something is not clear
+or you get stuck: it is more likely we did not do good enough a job at
+explaining things. So do not hesitate to open an issue, just to ask for
+clarification.
+
+### Style guide
 
 -   We use camelCase.
 
@@ -97,23 +87,31 @@ Here are the naming templates used.
 
 -   Behavior
 
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv`
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json`
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.tsv`
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.json`
+```bash
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.tsv
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.json
+```
 
 -   BOLD
 
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]`
+```bash
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
+```
 
 -   iEEG
 
-`sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json`
+```bash
+sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json
+```
 
 -   EEG
 
-`sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>`
-`sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.json`
+```bash
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.json
+```
 
 <!-- European data format (Each recording consisting of a .edf file)
 
@@ -132,14 +130,19 @@ Biosemi data format (Each recording consisting of a .bdf file) -->
 current format `<matches>_recording-eyetracking_physio.tsv.gz`
 
 future BEP format in a dedicated eyetracker folder
-`sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>`
+
+```bash
+sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>
+```
 
 -   Stim and physio
 
-`<matches>[_recording-<label>]_physio.tsv.gz`
-`<matches>[_recording-<label>]_physio.json`
-`<matches>[_recording-<label>]_stim.tsv.gz`
-`<matches>[_recording-<label>]_stim.json`
+```bash
+<matches>[_recording-<label>]_physio.tsv.gz
+<matches>[_recording-<label>]_physio.json
+<matches>[_recording-<label>]_stim.tsv.gz
+<matches>[_recording-<label>]_stim.json
+```
 
 ### Change log
 
@@ -164,6 +167,7 @@ Thanks goes to these wonderful people
 
 <!-- markdownlint-enable -->
 <!-- prettier-ignore-end -->
+
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
 This project follows the
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 00000000..d0c3cbf1
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/README.md b/docs/README.md
new file mode 100644
index 00000000..7d772758
--- /dev/null
+++ b/docs/README.md
@@ -0,0 +1,108 @@
+# Setting up sphinx to create a matlab doc
+
+## Set up virtual environment
+
+```bash
+virtualenv -p python3 cpp_bids
+source cpp_bids/bin/activate
+
+pip install -r requirements.txt
+```
+
+## Quick start on the doc
+
+See the [sphinx doc](https://www.sphinx-doc.org/en/master/usage/quickstart.html)
+for more.
+
+This
+[blog post](https://medium.com/@richdayandnight/a-simple-tutorial-on-how-to-document-your-python-project-using-sphinx-and-rinohtype-177c22a15b5b)
+is also useful.
+
+```bash
+cd docs
+sphinx-quickstart # launch a basic interactive set up of sphinx
+```
+
+Answer the questions on prompt.
+
+## Setting up conf.py for matlab doc
+
+Following the documentation from
+[matlabdomain for sphinx](https://github.com/sphinx-contrib/matlabdomain).
+
+Specify the extensions you are using:
+
+```python
+extensions = [
+    'sphinxcontrib.matlab',
+    'sphinx.ext.autodoc']
+```
+
+`matlab_src_dir` in `docs/source/conf.py` should have the path (relative to
+`conf.py`) to the folder containing your matlab code:
+
+```python
+matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
+```
+
+## reStructured text markup
+
+reStructured text mark up primers:
+
+-   on the [sphinx site](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html)
+
+-   more
+    [python oriented](https://pythonhosted.org/an_example_pypi_project/sphinx.html)
+
+-   typical doc strings templates
+    -   [google way](https://www.sphinx-doc.org/en/master/usage/extensions/example_google.html)
+    -   [numpy](https://www.sphinx-doc.org/en/master/usage/extensions/example_numpy.html#example-numpy)
+
+## "Templates"
+
+The templates to use for the doc are in the `src/templates` folder.
+
+You then just need to insert this in your `.rst` file for the documentation to
+be done automatically.
+
+```rst
+
+.. automodule:: src.folder_name .. <-- This is necessary for auto-documenting the rest
+
+.. autofunction:: function to document
+
+```
+
+To get the filenames of all the functions in a folder:
+
+``` bash
+ls -l src/*.m | cut -c42- | rev | cut -c 3- | rev
+```
+
+Increase the `42` to crop more characters at the beginning.
+
+Change the `3` to crop more characters at the end.
+
+## Build the documentation locally
+
+From the `docs` directory:
+
+```bash
+sphinx-build -b html source build
+```
+
+This will build an html version of the doc in the `build` folder.
+
+## Build the documentation with Read the Docs
+
+Add a [`.readthedocs.yml`](../.readthedocs.yml) file in the root of your repo.
+
+See [HERE](https://docs.readthedocs.io/en/stable/config-file/v2.html) for
+details.
+
+You can then trigger the build of the doc by going to the
+[read the docs website](https://readthedocs.org).
+
+You might need to be added as a maintainer of the doc.
+
+The doc can be built from any branch of a repo.
diff --git a/docs/functions-description.md b/docs/functions-description.md
deleted file mode 100644
index b6c3ab0d..00000000
--- a/docs/functions-description.md
+++ /dev/null
@@ -1,166 +0,0 @@
-# functions description
-
-<!-- lint disable -->
-
-<!-- TOC -->
-
--   [functions description](#functions-description)
-    -   [userInputs](#userinputs)
-    -   [createFilename](#createfilename)
-    -   [saveEventsFile](#saveeventsfile)
-    -   [checkCFG](#checkcfg)
-        -   [CFG content](#cfg-content)
-    -   [createBoldJson](#createboldjson)
-
-<!-- /TOC -->
-
-<!-- lint enable -->
-
-## userInputs
-
-Get subject, run and session number and make sure they are positive integer
-values.
-
-By default this will return `cfg.subject.session = 1` even if you asked it to
-omit enquiring about sessions. This means that the folder tree will always
-include a session folder.
-
-```matlab
-[cfg] = userInputs(cfg)
-```
-
-If you use it with `cfg.subject.askGrpSess = [0 0]`, it won't ask you about
-group or session.
-
-If you use it with `cfg.subject.askGrpSess = [1]`, it will only ask you about
-group
-
-If you use it with `cfg.subject.askGrpSess = [0 1]`, it will only ask you about
-session
-
-If you use it with `cfg.subject.askGrpSess = [1 1]`, it will ask you about both.
-This is the default behavior.
-
-## createFilename
-
-Create the BIDS compliant directories and filenames (but not the files) for the
-behavioral output for this subject / session / run.
-
-The folder tree will always include a session folder.
-
-It will also create the right filename for the eye-tracking data file if you ask
-it.
-
-For the moment the date of acquisition is appended to the filename
-
--   can work for behavioral experiment if `cfg.testingDevice` is set to `pc`,
--   can work for fMRI experiment if `cfg.testingDevice` is set to `mri`,
--   can work for simple eyetracking data if `cfg.eyeTracker.do` is set to 1.
-
-## saveEventsFile
-
-Function to save output files for events that will be BIDS compliant.
-
-If the user DOES NOT provide `onset`, `trial_type`, this events will be skipped.
-`duration` will be set to `n/a` if no value is provided.
-
-## checkCFG
-
-Check that we have all the fields that we need in the experiment parameters.
-
-### CFG content
-
-```matlab
-% The following can be modified by users but their effect might
-% only be effective after running checkCFG
-
-cfg.verbose = 0;
-
-cfg.subject.subjectGrp = '';
-cfg.subject.sessionNb = 1;
-cfg.subject.askGrpSess = [true true];
-
-% BOLD MRI details
-% some of those will be transferred to the correct fields in cfg.bids by checkCFG
-cfg.mri.repetitionTime = [];
-cfg.mri.contrastEnhancement = [];
-cfg.mri.phaseEncodingDirection = [];
-cfg.mri.reconstruction = [];
-cfg.mri.echo = [];
-cfg.mri.acquisition = [];
-
-cfg.fileName.task = '';
-cfg.fileName.zeroPadding = 3; % amount of 0 padding the subject, session, run number
-
-cfg.eyeTracker.do = false;
-
-% content of the json side-car file for bold data
-cfg.bids.mri.RepetitionTime = [];
-cfg.bids.mri.SliceTiming = '';
-cfg.bids.mri.TaskName = '';
-cfg.bids.mri.Instructions = '';
-cfg.bids.mri.TaskDescription = '';
-
-% content of the json side-car file for MEG
-cfg.bids.meg.TaskName = '';
-cfg.bids.meg.SamplingFrequency = [];
-cfg.bids.meg.PowerLineFrequency = [];
-cfg.bids.meg.DewarPosition = [];
-cfg.bids.meg.SoftwareFilters = [];
-cfg.bids.meg.DigitizedLandmarks = [];
-cfg.bids.meg.DigitizedHeadPoints = [];
-
-% content of the datasetDescription.json file
-cfg.bids.datasetDescription.Name = '';
-cfg.bids.datasetDescription.BIDSVersion =  '';
-cfg.bids.datasetDescription.License = '';
-cfg.bids.datasetDescription.Authors = {''};
-cfg.bids.datasetDescription.Acknowledgements = '';
-cfg.bids.datasetDescription.HowToAcknowledge = '';
-cfg.bids.datasetDescription.Funding = {''};
-cfg.bids.datasetDescription.ReferencesAndLinks = {''};
-cfg.bids.datasetDescription.DatasetDOI = '';
-
-
-%% Should not be modified by users
-% many of those fields are set up by checkCFG and you might get output that is not BIDS valid if you touch those
-cfg.fileName.dateFormat = 'yyyymmddHHMM'; % actual date of the experiment that is appended to the filename
-cfg.fileName.modality
-cgf.fileName.suffix.mri
-cgf.fileName.suffix.meg
-cfg.fileName.stim
-cfg.fileName.events
-cfg.fileName.datasetDescription
-
-```
-
-## createBoldJson
-
-```bash
-createBoldJson(cfg)
-```
-
-This function creates a very light-weight version of the side-car JSON file for
-a BOLD functional run.
-
-This will only contain the minimum BIDS requirement and will likely be less
-complete than the info you could from DICOM conversion.
-
-If you put the following line at the end of your experiment script, it will dump
-the content of the `extraInfo` structure in the json file.
-
-```bash
-createBoldJson(cfg, extraInfo)
-```
-
-This allows to add all the parameters that you used to run your experiment in a
-human readable format: so that when you write your methods sections 2 years
-later ("the reviewer asked me for the size of my fixation cross... FML"), the
-info you used WHEN you ran the experiment is saved in an easily accessible text
-format. For the love of the flying spaghetti monster do not save all your
-parameters in a `.mat` file: think of the case when you won't have matlab or
-octave installed on a computer (plus not everyone uses those).
-
-Also to reading your experiment parameters, you won't have to read it from the
-`setParameters.m` file and wonder if those might have been modified when running
-the experiment and you did not commit and tagged that change with git.
diff --git a/docs/installation.md b/docs/installation.md
index 89ed6d1c..3dfa9a5c 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -14,19 +14,22 @@
 
 <!-- lint enable -->
 
+## Use the CPP templates for PsychToolBox experiments
+
+The easiest way to use this repository is to create a new repository by using
+the
+[template PTB experiment repository](https://github.com/cpp-lln-lab/template_PTB_experiment):
+this creates a new repository on your github account with all the basic folders,
+files and submodules (including CPP_BIDS) already set up. You only have to then
+clone the repository and you are good to go.
+
 ## Download with git
 
 ```bash
 cd fullpath_to_directory_where_to_install
 
-# use git to download the code
-git clone https://github.com/cpp-lln-lab/CPP_BIDS.git
-
-# move into the folder you have just created
-cd CPP_BIDS
-
-# add the src folder to the matlab path and save the path
-matlab -nojvm -nosplash -r "addpath(fullfile(pwd, 'src')); savepath ();"
+# use git to download the code and the submodules
+git clone --recurse-submodules https://github.com/cpp-lln-lab/CPP_BIDS.git
 ```
 
 Then get the latest commit:
@@ -53,12 +56,6 @@ cd fullpath_to_directory_where_to_install
 
 # use git to download the code
 git submodule add https://github.com/cpp-lln-lab/CPP_BIDS.git
-
-# move into the folder you have just created
-cd CPP_BIDS
-
-# add the src folder to the matlab path and save the path
-matlab -nojvm -nosplash -r "addpath(fullfile(pwd, 'src'))"
 ```
 
 To get the latest commit you then need to update the submodule with the
@@ -83,7 +80,7 @@ git clone https://github.com/user_name/myExperiment.git
 # go into the directory
 cd myExperiment
 
-# initialize and get the content of the first level of submodules  (e.g. CPP_PTB and CPP_BIDS)
+# initialize and get the content of the first level of submodules
 git submodule init
 git submodule update
 
@@ -94,6 +91,8 @@ git submodule foreach --recursive 'git submodule update'
 
 ## Direct download
 
+NOT RECOMMENDED.
+
 Download the code. Unzip. And add to the matlab path.
 
 Pick a specific version from
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 00000000..9534b018
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/_static/cpp_lab_logo.png b/docs/source/_static/cpp_lab_logo.png
new file mode 100644
index 00000000..89277c01
Binary files /dev/null and b/docs/source/_static/cpp_lab_logo.png differ
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 00000000..5a423f71
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,91 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../..'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'CPP BIDS'
+copyright = '2020, the CPP BIDS dev team'
+author = 'the CPP BIDS dev team'
+
+# The full version, including alpha/beta/rc tags
+release = 'v1.0.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinxcontrib.matlab', 
+    'sphinx.ext.autodoc']
+matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
+primary_domain = 'mat'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# The master toctree document.
+master_doc = 'index'
+
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+html_logo = '_static/cpp_lab_logo.png'
+
+# html_theme_options = {
+#     'github_user': 'cpp-lln-lab',
+#     'github_repo': 'CPP_BIDS_SPM_pipeline',
+#     'github_button': True,
+#     'github_banner': True
+# }
+# html_theme_options = {
+#     'collapse_navigation': False,
+#     'display_version': False,
+#     'navigation_depth': 4,
+# }
+
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
\ No newline at end of file
diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
new file mode 100644
index 00000000..38d48d74
--- /dev/null
+++ b/docs/source/contributing.rst
@@ -0,0 +1,105 @@
+How to contribute to this project
+*********************************
+
+For more details please check the `contributing guidelines  <https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md>`_
+on the CPP lab's Github organization.
+
+
+Function templates
+==================
+
+.. automodule:: src.templates
+
+Template proposal
+-----------------
+
+::
+
+   % (C) Copyright 2020 CPP BIDS developers
+
+   function [argout1, argout2] = templateFunction(argin1, argin2, argin3)
+   %
+   % Short description of what the function does goes here.
+   %
+   % USAGE::
+   %
+   %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
+   %
+   % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet,
+   %                consectetur adipiscing elit. Ut congue nec est ac lacinia.
+   % :type argin1: type
+   % :param argin2: optional argument and its default value. And some of the
+   %               options can be shown in litteral like ``this`` or ``that``.
+   % :type argin2: string
+   % :param argin3: (dimension) optional argument
+   %
+   % :returns: - :argout1: (type) (dimension)
+   %           - :argout2: (type) (dimension)
+   %
+   % .. todo:
+   %
+   %    - item 1
+   %    - item 2
+
+   % The code goes below
+
+   end
+
+
+   end
+
+.. autofunction:: templateFunction  
+
+
+Example code in the help section
+--------------------------------
+
+::
+
+   % (C) Copyright 2020 CPP BIDS developers
+
+   function templateFunctionExample()
+   % This function illustrates a documentation test defined for MOdox.
+   % Other than that it does absolutely nothinghort description of what
+   % the function does goes here.
+   %
+   % Examples:
+   %   a=2;
+   %   disp(a)
+   %   % Expected output is prefixed by '%||' as in the following line:
+   %   %|| 2
+   %   %
+   %   % The test continues because no interruption through whitespace,
+   %   % as the previous line used a '%' comment character;
+   %   % thus the 'a' variable is still in the namespace and can be
+   %   % accessed.
+   %   b=3+a;
+   %   disp(a+[3 4])
+   %   %|| [5 6]
+   %
+   %   % A new test starts here because the previous line was white-space
+   %   % only. Thus the 'a' and 'b' variables are not present here anymore.
+   %   % The following expression raises an error because the 'b' variable
+   %   % is not defined (and does not carry over from the previous test).
+   %   % Because the expected output indicates an error as well,
+   %   % the test passes
+   %   disp(b)
+   %   %|| error('Some error')
+   %
+   %   % A set of expressions is ignored if there is no expected output
+   %   % (that is, no lines starting with '%||').
+   %   % Thus, the following expression is not part of any test,
+   %   % and therefore does not raise an error.
+   %   error('this is never executed)
+   %
+   %
+   % % tests end here because test indentation has ended
+
+   % The code goes below
+
+   end
+
+.. autofunction:: templateFunctionExample
+
+
+
diff --git a/docs/source/function_description.rst b/docs/source/function_description.rst
new file mode 100644
index 00000000..6db43466
--- /dev/null
+++ b/docs/source/function_description.rst
@@ -0,0 +1,34 @@
+Function description
+********************
+  
+List of functions in the ``src`` folder.  
+
+----
+
+.. automodule:: src 
+
+.. autofunction:: convertSourceToRaw
+.. autofunction:: createDataDictionary
+.. autofunction:: createDatasetDescription
+.. autofunction:: createFilename
+.. autofunction:: createJson
+
+``createJson`` can be used to save in a
+human readable format the extra parameters that you used to run your experiment. 
+This will most likely make the json file non-bids compliant but it can prove useful,
+to keep this information in your source dataset
+for when you write your methods sections 2 years later after running the experiment.
+This ensures that those are the exact parameters you used and you won't have 
+to read them from the ``setParameters.m`` file and wonder 
+if those might have been modified when running the experiment 
+and you did not commit and tagged that change with git.
+
+And for the love of the flying spaghetti monster do not save all your
+parameters in a `.mat` file: think of the case when you won't have Matlab or
+Octave installed on a computer (plus not everyone uses those).
+
+.. autofunction:: readAndFilterLogfile
+.. autofunction:: saveEventsFile
+.. autofunction:: userInputs
+
+
diff --git a/docs/source/gui.rst b/docs/source/gui.rst
new file mode 100644
index 00000000..3852af8a
--- /dev/null
+++ b/docs/source/gui.rst
@@ -0,0 +1,17 @@
+Graphic interface
+*****************
+  
+List of functions in the ``gui`` folder: those are mostly to handle the "graphic interface"
+that can be used to deal with ``userInputs()``.
+
+----
+
+.. automodule:: src.gui 
+
+.. autofunction:: askForGroupAndOrSession
+.. autofunction:: askUserGui
+.. autofunction:: createQuestionList
+.. autofunction:: getIsQuestionToAsk
+.. autofunction:: setDefaultResponses
+
+
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 00000000..b663cb83
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,58 @@
+.. cpp_bids documentation master file
+
+Welcome to CPP BIDS documentation!
+**********************************
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Content
+
+   set_up
+   function_description
+   utilities
+   gui
+   contributing
+
+A set of function for matlab and octave to create
+`BIDS-compatible <https://bids-specification.readthedocs.io/en/stable/>`_
+structure and filenames for the output of behavioral, EEG, fMRI, eyetracking
+experiments.
+
+Output format
+=============
+
+Modality agnostic aspect
+------------------------
+
+The files created by this toolbox will always follow the following pattern::
+
+  dataDir/sub-<[Group]SubNb>/ses-sesNb/sub-<[Group]SubNb>_ses-<sesNb>_task-<taskName>*_modality_date-*.fileExtension
+
+Subjects, session and run number labels will be numbers with zero padding up (default is set to
+3, meaning that subject 1 will become ``sub-001``).
+
+The ``Group`` name is optional.
+
+A session folder will ALWAYS be created even if not requested (default will be ``ses-001``).
+
+Task labels will be printed in ``camelCase`` in the filenames.
+
+Time stamps are added directly in the filename by adding a suffix
+``_date-*`` (default format is ``YYYYMMDDHHMM``) which makes the file name non-BIDS compliant. 
+This was added to prevent overwriting files in case a certain run needs to be done 
+a second time because of a crash. 
+Some of us are paranoid about keeping even cancelled runs during my experiments. 
+This suffix should be removed to make the data set BIDS compliant. 
+See ``convertSourceToRaw()`` for more details.
+
+For example::
+
+  /user/bob/dataset002/sub-090/ses-003/sub-090_ses-003_task-auditoryTask_run-023_events_date-202007291536.tsv
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/set_up.rst b/docs/source/set_up.rst
new file mode 100644
index 00000000..41c9edfb
--- /dev/null
+++ b/docs/source/set_up.rst
@@ -0,0 +1,53 @@
+Setting up your experiment
+**************************
+
+Configuration
+=============
+
+.. todo:
+   describe how to set things up
+
+
+.. automodule:: src
+.. autofunction:: checkCFG
+
+.. automodule:: src.utils
+.. autofunction:: transferInfoToBids
+
+.. todo:
+    0: almost nothing gets printed on screen
+    1: allows saveEvents to print stuff when saving to file or createFilename to tell you where things will be saved
+    2: let printCredits do its job and lets saveEvents print extra info when it sends some warning.
+
+Group, subject, session and run
+===============================
+
+You can use the ``userInputs()`` function to easily set the group name as well as
+the subject, session and run number. You can ask the function to not bother you with 
+group and session 
+
+
+.. todo:
+
+    Get subject, run and session number and make sure they are positive integer
+    values.
+
+    By default this will return `cfg.subject.session = 1` even if you asked it to
+    omit enquiring about sessions. This means that the folder tree will always
+    include a session folder.
+
+    ```matlab
+    [cfg] = userInputs(cfg)
+    ```
+
+    If you use it with `cfg.subject.askGrpSess = [0 0]`, it won't ask you about
+    group or session.
+
+    If you use it with `cfg.subject.askGrpSess = [1]`, it will only ask you about
+    group
+
+    If you use it with `cfg.subject.askGrpSess = [0 1]`, it will only ask you about
+    session
+
+    If you use it with `cfg.subject.askGrpSess = [1 1]`, it will ask you about both.
+    This is the default behavior.
\ No newline at end of file
diff --git a/docs/source/utilities.rst b/docs/source/utilities.rst
new file mode 100644
index 00000000..7821160d
--- /dev/null
+++ b/docs/source/utilities.rst
@@ -0,0 +1,27 @@
+Utility functions
+*****************
+  
+List of functions in the ``utils`` folder.  
+
+----
+
+.. automodule:: src.utils
+
+.. autofunction:: checkCppBidsDependencies
+.. autofunction:: checkInput
+.. autofunction:: createValidName
+.. autofunction:: getFullFilename
+.. autofunction:: initializeExtraColumns
+.. autofunction:: isPositiveInteger
+.. autofunction:: nanPadding
+.. autofunction:: printCreditsCppBids
+.. autofunction:: removeAllDateSuffix
+.. autofunction:: removeDateSuffix
+.. autofunction:: returnHeaderName
+.. autofunction:: returnNamesExtraColumns
+.. autofunction:: returnNbColumns
+.. autofunction:: setDefaultFields
+
+.. automodule:: src.gui 
+
+.. autofunction:: askUserCli
diff --git a/lib/bids-matlab b/lib/bids-matlab
index bda01141..d0815ea7 160000
--- a/lib/bids-matlab
+++ b/lib/bids-matlab
@@ -1 +1 @@
-Subproject commit bda011411defe36c00d1d501b6842fd677af32fc
+Subproject commit d0815ea702ea85ba9348ab2780f84564fbd5520f
diff --git a/lib/utils/abspath.m b/lib/utils/abspath.m
new file mode 100644
index 00000000..4376fc4f
--- /dev/null
+++ b/lib/utils/abspath.m
@@ -0,0 +1,117 @@
+function fpath = abspath(fpath)
+%ABSPATH  Converts path to an absolute path
+%
+%   Converts a relative path from the current working directory to an
+%   absolute path by glueing the pwd and the relative path together and
+%   eliminating relative references like '.' and '..'. If the provided path
+%   is already absolute, only the references like '.' and '..' are removed.
+%
+%   Syntax:
+%   fpath = abspath(fpath)
+%
+%   Input:
+%   fpath   = path to be converted
+%
+%   Output:
+%   fpath   = absolute path
+%
+%   Example
+%   fpath = abspath(fpath)
+%
+%   See also 
+
+%% Copyright notice
+%   --------------------------------------------------------------------
+%   Copyright (C) 2010 Deltares
+%       Bas Hoonhout
+%
+%       bas.hoonhout@deltares.nl	
+%
+%       Rotterdamseweg 185
+%       2629HD Delft
+%
+%   This library is free software: you can redistribute it and/or
+%   modify it under the terms of the GNU Lesser General Public
+%   License as published by the Free Software Foundation, either
+%   version 2.1 of the License, or (at your option) any later version.
+%
+%   This library is distributed in the hope that it will be useful,
+%   but WITHOUT ANY WARRANTY; without even the implied warranty of
+%   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+%   Lesser General Public License for more details.
+%
+%   You should have received a copy of the GNU Lesser General Public
+%   License along with this library. If not, see <http://www.gnu.org/licenses/>.
+%   --------------------------------------------------------------------
+
+% This tool is part of <a href="http://OpenEarth.nl">OpenEarthTools</a>.
+% OpenEarthTools is an online collaboration to share and manage data and 
+% programming tools in an open source, version controlled environment.
+% Sign up to recieve regular updates of this function, and to contribute 
+% your own tools.
+
+%% Version <http://svnbook.red-bean.com/en/1.5/svn.advanced.props.special.keywords.html>
+% Created: 24 Nov 2010
+% Created with Matlab version: 7.9.0.529 (R2009b)
+
+% $Id$
+% $Date$
+% $Author$
+% $Revision$
+% $HeadURL$
+% $Keywords: $
+
+%% convert to absolute path
+% make sure fileseperators are right
+fpath = fullfile(fpath, '');
+
+% check if path is relative
+isRelative = false;
+if ispc()
+    if length(fpath) < 2 || ...
+            (fpath(2) ~= ':' && ~strcmpi(repmat(filesep,1,2), fpath(1:2)))
+        isRelative = true;
+    end
+elseif isunix()
+    if ~any(strcmp(fpath(1), {filesep '~'}))
+        isRelative = true;
+    end
+else
+    error('Unsupported operating system');
+end
+
+if isRelative
+    fpath = fullfile(pwd, fpath);
+end
+
+if ispc()
+    root  = fpath(1:2);
+    fpath = fpath(3:end);
+elseif isunix()
+    root  = fpath(1);
+    fpath = fpath(2:end);
+end
+
+p = regexp(fpath, filesep, 'split');
+
+% remove '.' elements
+p = p(~strcmp(p, '.'));
+
+% replace relative references
+i = 1;
+while i <= length(p)
+    if strcmp(p{i}, '..')
+        p(i-1:i) = [];
+        i = i-2;
+    end
+    i = i+1;
+end
+
+% glue path together
+fpath = fullfile(root, p{:}, '');
+
+% help unix users
+if isunix && ...
+        (isempty(fpath) || ~strcmp(fpath(1), '~'))
+    fpath = [filesep fpath];
+end
\ No newline at end of file
diff --git a/manualTests/miss_hit.cfg b/manualTests/miss_hit.cfg
index f59bdb02..d86aaeb0 100644
--- a/manualTests/miss_hit.cfg
+++ b/manualTests/miss_hit.cfg
@@ -1,7 +1,6 @@
 # style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
-suppress_rule: "copyright_notice"
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 4
diff --git a/manualTests/test_createDataDictionary.m b/manualTests/test_createDataDictionary.m
deleted file mode 100644
index 48611447..00000000
--- a/manualTests/test_createDataDictionary.m
+++ /dev/null
@@ -1,55 +0,0 @@
-function test_suite = test_createDataDictionary %#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_createDataDictionaryBasic()
-
-    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-
-    %% set up
-
-    cfg.verbose = false;
-
-    cfg.subject.subjectNb = 1;
-    cfg.subject.runNb = 1;
-
-    cfg.task.name = 'testtask';
-
-    cfg.dir.output = outputDir;
-
-    cfg.testingDevice = 'mri';
-
-    cfg = createFilename(cfg);
-
-    logFile.extraColumns.Speed.length = 1;
-    logFile.extraColumns.LHL24.length = 3;
-    logFile = saveEventsFile('init', cfg, logFile);
-
-    createDataDictionary(cfg, logFile);
-
-    %% check that the file has the right path and name
-
-    % data to test against
-    funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
-
-    jsonFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
-                    cfg.fileName.date '.json'];
-
-    % test
-    assertTrue(exist(fullfile(funcDir, jsonFilename), 'file') == 2);
-
-    %% check content
-    actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
-
-    % data to test against
-    expectedStruct = bids.util.jsondecode( ...
-                                          fullfile(pwd, 'testData', 'eventsDataDictionary.json'));
-
-    % test
-    assertTrue(isequal(expectedStruct, actualStruct));
-
-end
diff --git a/manualTests/test_createJson.m b/manualTests/test_createJson.m
deleted file mode 100644
index 47fbd6ad..00000000
--- a/manualTests/test_createJson.m
+++ /dev/null
@@ -1,50 +0,0 @@
-function test_suite = test_createJson %#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_createJsonExtra()
-
-    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
-
-    %% set up
-
-    cfg.verbose = false;
-
-    cfg.subject.subjectNb = 1;
-    cfg.subject.runNb = 1;
-
-    cfg.task.name = 'testtask';
-
-    cfg.dir.output = outputDir;
-
-    cfg.testingDevice = 'mri';
-
-    cfg = createFilename(cfg);
-
-    logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
-
-    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
-
-    createJson(cfg, extraInfo);
-
-    %% check content
-    fileName = strrep(cfg.fileName.events, '_events', '_bold');
-    fileName = strrep(fileName, '.tsv', '.json');
-
-    actualStruct = bids.util.jsondecode(fullfile( ...
-                                                 cfg.dir.outputSubject, ...
-                                                 cfg.fileName.modality, ...
-                                                 fileName));
-
-    % data to test against
-    expectedStruct = bids.util.jsondecode( ...
-                                          fullfile(pwd, 'testData', 'extra_bold.json'));
-
-    % test
-    assertEqual(expectedStruct, actualStruct);
-
-end
diff --git a/manualTests/test_makeRawDataset.m b/manualTests/test_makeRawDataset.m
index 485a912d..7008843f 100644
--- a/manualTests/test_makeRawDataset.m
+++ b/manualTests/test_makeRawDataset.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_makeRawDataset()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
@@ -24,11 +26,15 @@ function test_makeRawDataset()
     cfg.task.name = 'testtask';
     cfg.task.instructions = 'do this';
 
+    cfg.verbosity = 0;
+
+    cfg = createFilename(cfg);
+
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
     logFile.extraColumns.is_Fixation.length = 1;
 
-    cfg = createFilename(cfg);
+    logFile = saveEventsFile('init', cfg, logFile);
 
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
     createJson(cfg, extraInfo);
@@ -71,14 +77,22 @@ function test_makeRawDataset()
     saveEventsFile('close', cfg, logFile);
 
     % add dummy stim data
-    stimLogFile = saveEventsFile('open_stim', cfg, logFile);
+    stimLogFile.extraColumns.Speed.length = 1;
+    stimLogFile.extraColumns.LHL24.length = 1;
+    stimLogFile.extraColumns.is_Fixation.length = 1;
+
+    stimLogFile.SamplingFrequency = cfg.mri.repetitionTime;
+    stimLogFile.StartTime = 0;
+
+    stimLogFile = saveEventsFile('init_stim', cfg, stimLogFile);
+    stimLogFile = saveEventsFile('open', cfg, stimLogFile);
     for i = 1:100
         stimLogFile(i, 1).onset = cfg.mri.repetitionTime * i;
         stimLogFile(i, 1).trial_type = 'test';
         stimLogFile(i, 1).duration = 1;
         stimLogFile(i, 1).Speed = rand(1);
         stimLogFile(i, 1).is_Fixation = rand > 0.5;
-        stimLogFile(i, 1).LHL24 = randn(1, 3);
+        stimLogFile(i, 1).LHL24 = randn();
     end
     saveEventsFile('save', cfg, stimLogFile);
     saveEventsFile('close', cfg, stimLogFile);
diff --git a/notebooks/basic_usage.ipynb b/notebooks/basic_usage.ipynb
index 595c05a8..47aca2e9 100644
--- a/notebooks/basic_usage.ipynb
+++ b/notebooks/basic_usage.ipynb
@@ -1,13 +1,21 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Basic usage"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
-    "% add the relevant functions from the src folder\n",
-    "addpath(genpath(fullfile(pwd, '..', 'src')))"
+    "% add the relevant functions from the source and library folder\n",
+    "addpath(genpath(fullfile(pwd, '..', 'src')))\n",
+    "addpath(genpath(fullfile(pwd, '..', 'lib')))"
    ]
   },
   {
@@ -16,7 +24,7 @@
    "source": [
     "## Setting the parameters about our experiment\n",
     "\n",
-    "We need to define the configuration structure where we put all our information."
+    "We need to define the configuration structure where we put the information about the experiment."
    ]
   },
   {
@@ -28,41 +36,40 @@
     "% define the folder where the data will be saved\n",
     "cfg.dir.output = fullfile(pwd, 'output');\n",
     "\n",
+    "cfg.verbose = 1;\n",
+    "\n",
     "% define the name of the task\n",
     "cfg.task.name = 'test task';\n",
     "\n",
-    "% can use the userInputs function to collect subject info\n",
+    "% We can use the userInputs function to collect subject info: this won't work in a jupyter notebook though\n",
     "% cfg = userInputs;\n",
     "\n",
-    "% Or we can add those information manually directly\n",
+    "% so we can add those information manually directly\n",
     "cfg.subject.subjectNb = 1;\n",
     "cfg.subject.runNb = 1;\n",
     "\n",
     "% if set to 'mri' then the data will be saved in the `func` folder\n",
-    "cfg.testingDevice = 'mri';\n",
-    "\n",
-    "% to keep things quiet\n",
-    "cfg.verbose = false;\n"
+    "cfg.testingDevice = 'mri';"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If set to `eeg` then the data will be saved in the `eeg` folder\n",
-    "\n",
-    "```\n",
-    "cfg.testingDevice = 'eeg';\n",
-    "```\n",
-    "\n",
-    "By default we assume you are running things on a behavioral PC with no eyetracker.\n",
+    "By default we assume you are running a purely behavioral experiment with no eyetracker.\n",
     "\n",
     "```\n",
     "cfg.eyeTracker = false;\n",
     "cfg.testingDevice = 'pc';\n",
     "```\n",
     "\n",
-    "If the testing device is set to `pc` then the data will be saved in the `beh` folder"
+    "If the testing device is set to `pc` then the data will be saved in the `beh` folder\n",
+    "\n",
+    "If set to `eeg` then the data will be saved in the `eeg` folder\n",
+    "\n",
+    "```\n",
+    "cfg.testingDevice = 'eeg';\n",
+    "```"
    ]
   },
   {
@@ -74,110 +81,41 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "cfg =\r\n",
-      "\r\n",
-      "  scalar structure containing the fields:\r\n",
-      "\r\n",
-      "    bids =\r\n",
-      "\r\n",
-      "      scalar structure containing the fields:\r\n",
-      "\r\n",
-      "        datasetDescription =\r\n",
-      "\r\n",
-      "          scalar structure containing the fields:\r\n",
-      "\r\n",
-      "            Acknowledgements: 0x0 sq_string\r\n",
-      "            Authors: 1x1 cell\r\n",
-      "            BIDSVersion: 0x0 sq_string\r\n",
-      "            DatasetDOI: 0x0 sq_string\r\n",
-      "            Funding: 1x1 cell\r\n",
-      "            HowToAcknowledge: 0x0 sq_string\r\n",
-      "            License: 0x0 sq_string\r\n",
-      "            Name: 0x0 sq_string\r\n",
-      "            ReferencesAndLinks: 1x1 cell\r\n",
-      "\r\n",
-      "        mri =\r\n",
-      "\r\n",
-      "          scalar structure containing the fields:\r\n",
-      "\r\n",
-      "            Instructions: 0x0 sq_string\r\n",
-      "            RepetitionTime: 0x0 matrix\r\n",
-      "            SliceTiming: 0x0 matrix\r\n",
-      "            TaskDescription: 0x0 sq_string\r\n",
-      "            TaskName: 1x9 sq_string\r\n",
-      "\r\n",
-      "        meg =\r\n",
-      "\r\n",
-      "          scalar structure containing the fields:\r\n",
-      "\r\n",
-      "            DewarPosition: 0x0 matrix\r\n",
-      "            DigitizedHeadPoints: 0x0 matrix\r\n",
-      "            DigitizedLandmarks: 0x0 matrix\r\n",
-      "            PowerLineFrequency: 0x0 matrix\r\n",
-      "            SamplingFrequency: 0x0 matrix\r\n",
-      "            SoftwareFilters: 0x0 matrix\r\n",
-      "            TaskName: 1x9 sq_string\r\n",
-      "\r\n",
       "\r\n",
-      "    dir =\r\n",
       "\r\n",
-      "      scalar structure containing the fields:\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "                                                   \r\n",
+      "         ___ ___ ___   ___ ___ ___  ___            \r\n",
+      "        / __| _ \\ _ \\ | _ )_ _|   \\/ __|\r\n",
+      "       | (__|  _/  _/ | _ \\| || |) \\__ \\\r\n",
+      "        \\___|_| |_|   |___/___|___/|___/\r\n",
+      "                                                   \r\n",
+      "Thank you for using the CPP BIDS - version v1.0.0. \r\n",
       "\r\n",
-      "        output = /home/remi/github/CPP_BIDS/notebooks/output\r\n",
+      "Current list of contributors includes:\r\n",
+      " Rémi Gau\r\n",
+      " Marco Barilari\r\n",
+      " Ceren Battal\r\n",
+      " Tomas Lenc\r\n",
+      "\b\r\n",
       "\r\n",
-      "    eyeTracker =\r\n",
+      "Please cite using the following DOI: \r\n",
+      " https://doi.org/10.5281/zenodo.4007674\r\n",
       "\r\n",
-      "      scalar structure containing the fields:\r\n",
+      "For bug report, suggestions or contributions see: \r\n",
+      " https://github.com/cpp-lln-lab/CPP_BIDS\r\n",
       "\r\n",
-      "        do = 0\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
       "\r\n",
-      "    fileName =\r\n",
-      "\r\n",
-      "      scalar structure containing the fields:\r\n",
-      "\r\n",
-      "        task = testTask\r\n",
-      "        zeroPadding =  3\r\n",
-      "        dateFormat = yyyymmddHHMM\r\n",
-      "\r\n",
-      "    mri =\r\n",
-      "\r\n",
-      "      scalar structure containing the fields:\r\n",
-      "\r\n",
-      "        acquisition = [](0x0)\r\n",
-      "        contrastEnhancement = [](0x0)\r\n",
-      "        echo = [](0x0)\r\n",
-      "        phaseEncodingDirection = [](0x0)\r\n",
-      "        reconstruction = [](0x0)\r\n",
-      "        repetitionTime = [](0x0)\r\n",
-      "\r\n",
-      "    subject =\r\n",
-      "\r\n",
-      "      scalar structure containing the fields:\r\n",
-      "\r\n",
-      "        askGrpSess =\r\n",
-      "\r\n",
-      "          1  1\r\n",
-      "\r\n",
-      "        runNb =  1\r\n",
-      "        sessionNb =  1\r\n",
-      "        subjectGrp = \r\n",
-      "        subjectNb =  1\r\n",
-      "\r\n",
-      "    task =\r\n",
-      "\r\n",
-      "      scalar structure containing the fields:\r\n",
-      "\r\n",
-      "        name = test task\r\n",
-      "\r\n",
-      "    testingDevice = mri\r\n",
-      "    verbose = 0\r\n",
       "\r\n"
      ]
     }
    ],
    "source": [
     "% We can then initialize all the other fields. The ones we have already filled in will not be overwritten\n",
-    "cfg = checkCFG(cfg)"
+    "cfg = checkCFG(cfg);"
    ]
   },
   {
@@ -195,7 +133,7 @@
    "source": [
     "% create the filenames: this include a step to check that all the information is there: createFilename calls \n",
     "% checkCFG before running\n",
-    "[cfg] = createFilename(cfg);"
+    "cfg = createFilename(cfg);"
    ]
   },
   {
@@ -220,12 +158,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ans = /home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001\r\n"
+      "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001\r\n"
      ]
     }
    ],
    "source": [
-    "cfg.dir.outputSubject"
+    "disp(cfg.dir.outputSubject)"
    ]
   },
   {
@@ -248,12 +186,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ans = sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n"
+      "sub-001_ses-001_task-testTask_run-001_events_date-202011171229.tsv\r\n"
      ]
     }
    ],
    "source": [
-    "cfg.fileName.events"
+    "disp(cfg.fileName.events)"
    ]
   },
   {
@@ -272,15 +210,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ans = /home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n"
+      "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202011171229.tsv\r\n"
      ]
     }
    ],
    "source": [
-    "fullfile(...\n",
+    "disp(fullfile(...\n",
     "    cfg.dir.outputSubject, ...\n",
     "    cfg.fileName.modality, ...\n",
-    "    cfg.fileName.events)"
+    "    cfg.fileName.events))"
    ]
   },
   {
@@ -303,10 +241,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "clear cfg\n",
+    "clear cfg logFile\n",
     "\n",
     "cfg.dir.output = fullfile(pwd, 'output');\n",
     "\n",
+    "cfg.verbose = 0;\n",
+    "\n",
     "cfg.task.name = 'test task';\n",
     "\n",
     "cfg.subject.subjectNb = 1;\n",
@@ -314,13 +254,11 @@
     "\n",
     "cfg.testingDevice = 'mri';\n",
     "\n",
-    "cfg.verbose = false;\n",
-    "\n",
     "% Create the filenames\n",
     "[cfg] = createFilename(cfg);\n",
     "\n",
     "% We can define what extra columns we want in our tsv file beyond the \n",
-    "% BIDS holy trinity ('onset', 'duration', 'trial_type')\n",
+    "% BIDS \"holy trinity\" ('onset', 'duration', 'trial_type')\n",
     "\n",
     "% Say we want to keep track of the type of target that what presented during a trial and of its position\n",
     "logFile.extraColumns = {'target_position', 'target_type'};\n"
@@ -348,7 +286,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This will initialize a structure for each extra column."
+    "This will initialize a structure for each extra column.\n"
    ]
   },
   {
@@ -362,7 +300,6 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ans =\r\n",
       "\r\n",
       "  scalar structure containing the fields:\r\n",
       "\r\n",
@@ -370,12 +307,12 @@
       "    Levels = \r\n",
       "    LongName = \r\n",
       "    TermURL = \r\n",
-      "\r\n"
+      "    Units = \r\n"
      ]
     }
    ],
    "source": [
-    "logFile.extraColumns.target_position.bids"
+    "disp(logFile.extraColumns.target_position.bids)"
    ]
   },
   {
@@ -394,7 +331,6 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ans =\r\n",
       "\r\n",
       "  scalar structure containing the fields:\r\n",
       "\r\n",
@@ -407,7 +343,7 @@
       "    }\r\n",
       "    LongName = \r\n",
       "    TermURL = \r\n",
-      "\r\n"
+      "    Units = \r\n"
      ]
     }
    ],
@@ -415,7 +351,7 @@
     "logFile.extraColumns.target_position.bids.Description = 'Position of the target on the screen';\n",
     "logFile.extraColumns.target_position.bids.Levels = {'left', 'center', 'right'};\n",
     "\n",
-    "logFile.extraColumns.target_position.bids"
+    "disp(logFile.extraColumns.target_position.bids)"
    ]
   },
   {
@@ -471,33 +407,17 @@
       "├── basic_usage.ipynb\r\n",
       "├── creating_BIDS_dataset.ipynb\r\n",
       "├── more_on_saving.ipynb\r\n",
-      "├── octave-workspace\r\n",
       "├── \u001b[01;34moutput\u001b[00m\r\n",
-      "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n",
-      "│   │   ├── CHANGES\r\n",
-      "│   │   ├── dataset_description.json\r\n",
-      "│   │   ├── README\r\n",
-      "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n",
-      "│   │       └── \u001b[01;34mses-001\u001b[00m\r\n",
-      "│   │           └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n",
-      "│   │               └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n",
       "│   └── \u001b[01;34msource\u001b[00m\r\n",
-      "│       ├── CHANGES\r\n",
-      "│       ├── dataset_description.json\r\n",
-      "│       ├── README\r\n",
       "│       └── \u001b[01;34msub-001\u001b[00m\r\n",
       "│           └── \u001b[01;34mses-001\u001b[00m\r\n",
       "│               └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n",
-      "│                   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n",
-      "└── README.md\r\n",
+      "│                   ├── sub-001_ses-001_task-testTask_run-001_events_date-202011171229.json\r\n",
+      "│                   └── sub-001_ses-001_task-testTask_run-001_events_date-202011171229.tsv\r\n",
+      "├── README.md\r\n",
+      "└── using_2_logfiles.ipynb\r\n",
       "\r\n",
-      "9 directories, 19 files\r\n",
+      "5 directories, 7 files\r\n",
       "\n"
      ]
     }
@@ -531,7 +451,7 @@
       "{\r\n",
       "    \"onset\": {\r\n",
       "        \"Description\": \"time elapsed since experiment start\",\r\n",
-      "        \"Unit\": \"s\"\r\n",
+      "        \"Units\": \"s\"\r\n",
       "    },\r\n",
       "    \"trial_type\": {\r\n",
       "        \"Description\": \"types of trial\",\r\n",
@@ -539,7 +459,7 @@
       "    },\r\n",
       "    \"duration\": {\r\n",
       "        \"Description\": \"duration of the event or the block\",\r\n",
-      "        \"Unit\": \"s\"\r\n",
+      "        \"Units\": \"s\"\r\n",
       "    },\r\n",
       "    \"target_position\": {\r\n",
       "        \"Description\": \"Position of the target on the screen\",\r\n",
@@ -549,13 +469,15 @@
       "            \"right\"\r\n",
       "        ],\r\n",
       "        \"LongName\": \"\",\r\n",
-      "        \"TermURL\": \"\"\r\n",
+      "        \"TermURL\": \"\",\r\n",
+      "        \"Units\": \"\"\r\n",
       "    },\r\n",
       "    \"target_type\": {\r\n",
       "        \"Description\": \"\",\r\n",
       "        \"Levels\": \"\",\r\n",
       "        \"LongName\": \"\",\r\n",
-      "        \"TermURL\": \"\"\r\n",
+      "        \"TermURL\": \"\",\r\n",
+      "        \"Units\": \"\"\r\n",
       "    }\r\n",
       "}\n"
      ]
@@ -574,14 +496,18 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2.000000\t1.000000\tmotion_up\tleft\taudio\t\r\n",
-      "6.000000\t1.200000\tstatic\tright\tvisual\t\r\n"
+      "ans =  2\r\n",
+      "ans =  1\r\n",
+      "\r\n",
+      "ans =  6\r\n",
+      "ans =  1.2000\r\n",
+      "\r\n"
      ]
     }
    ],
    "source": [
     "% The information about 2 events that we want to save\n",
-    "% NOTE : If the user DOES NOT provide `onset`, `trial_type`, this events will be skipped.\n",
+    "% NOTE : If the user DOES NOT provide `onset`, `duration`, this events will be skipped.\n",
     "\n",
     "% Trial one\n",
     "logFile(1,1).onset = 2;\n",
@@ -618,10 +544,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "warning: \r\n",
-      "Skipping saving this event.\r\n",
+      "warning: Skipping saving this event. \r\n",
       " onset: NaN \r\n",
-      " duration: NaN\r\n"
+      " duration: NaN \r\n"
      ]
     }
    ],
@@ -649,11 +574,13 @@
      "text": [
       "warning: Missing some target_position data for this event.\r\n",
       "warning: called from\r\n",
-      "    saveEventsFile>checkExtracolumns at line 219 column 13\r\n",
-      "    saveEventsFile>checklLogFile at line 140 column 21\r\n",
-      "    saveEventsFile>saveToLogFile at line 282 column 17\r\n",
-      "    saveEventsFile at line 90 column 21\r\n",
-      "10.000000\t1.000000\tmotion_down\tn/a\taudio\t\r\n"
+      "    saveEventsFile>checkExtracolumns at line 288 column 13\r\n",
+      "    saveEventsFile>checklLogFile at line 173 column 21\r\n",
+      "    saveEventsFile>saveToLogFile at line 351 column 17\r\n",
+      "    saveEventsFile at line 123 column 21\r\n",
+      "ans =  10\r\n",
+      "ans =  1\r\n",
+      "\r\n"
      ]
     }
    ],
@@ -679,22 +606,9 @@
    "cell_type": "code",
    "execution_count": 18,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\r\n",
-      "Data were saved in this file:\r\n",
-      "\r\n",
-      "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n",
-      "\r\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "% close the file\n",
-    "cfg.verbose = true; % set verbose in true if you want to know where things are\n",
     "saveEventsFile('close', cfg, logFile);"
    ]
   },
diff --git a/notebooks/creating_BIDS_dataset.ipynb b/notebooks/creating_BIDS_dataset.ipynb
index 9141308c..7cc44047 100644
--- a/notebooks/creating_BIDS_dataset.ipynb
+++ b/notebooks/creating_BIDS_dataset.ipynb
@@ -16,12 +16,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 33,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "addpath(genpath(fullfile(pwd, '..', 'src')))\n",
+    "addpath(genpath(fullfile(pwd, '..', 'lib')))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 34,
    "metadata": {},
    "outputs": [],
    "source": [
-    "addpath(genpath(fullfile(pwd, '..', 'src')));\n",
-    "\n",
     "cfg.dir.output = fullfile(pwd, 'output');\n",
     "\n",
     "cfg.task.name = 'test task';\n",
@@ -33,14 +41,56 @@
     "\n",
     "cfg.eyetracker.do = 1;\n",
     "\n",
-    "cfg.verbose = false;"
+    "cfg.verbose = 2;"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 35,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\r\n",
+      "\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "                                                   \r\n",
+      "         ___ ___ ___   ___ ___ ___  ___            \r\n",
+      "        / __| _ \\ _ \\ | _ )_ _|   \\/ __|\r\n",
+      "       | (__|  _/  _/ | _ \\| || |) \\__ \\\r\n",
+      "        \\___|_| |_|   |___/___|___/|___/\r\n",
+      "                                                   \r\n",
+      "Thank you for using the CPP BIDS - version v1.0.0. \r\n",
+      "\r\n",
+      "Current list of contributors includes:\r\n",
+      " Rémi Gau\r\n",
+      " Marco Barilari\r\n",
+      " Ceren Battal\r\n",
+      " Tomas Lenc\r\n",
+      "\b\r\n",
+      "\r\n",
+      "Please cite using the following DOI: \r\n",
+      " https://doi.org/10.5281/zenodo.4007674\r\n",
+      "\r\n",
+      "For bug report, suggestions or contributions see: \r\n",
+      " https://github.com/cpp-lln-lab/CPP_BIDS\r\n",
+      "\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "\r\n",
+      "\r\n",
+      "\r\n",
+      "Data will be saved in this directory:\r\n",
+      "\t/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func\r\n",
+      "\r\n",
+      "Data will be saved in this file:\r\n",
+      "\tsub-001_ses-001_task-testTask_run-001_events_date-202011171530.tsv\r\n"
+     ]
+    }
+   ],
    "source": [
     "cfg.bids.datasetDescription.Name = 'my new bids data set';\n",
     "cfg.bids.datasetDescription.BIDSVersion =  '1.3';\n",
@@ -57,66 +107,41 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 36,
    "metadata": {},
    "outputs": [],
    "source": [
-    "mkdir(fullfile(cfg.dir.outputSubject, cfg.fileName.modality));\n",
-    "\n",
     "createDatasetDescription(cfg)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 37,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[01;34m.\u001b[00m\r\n",
-      "├── basic_usage.ipynb\r\n",
-      "├── creating_BIDS_dataset.ipynb\r\n",
-      "├── more_on_saving.ipynb\r\n",
-      "├── octave-workspace\r\n",
-      "├── \u001b[01;34moutput\u001b[00m\r\n",
-      "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n",
-      "│   │   ├── CHANGES\r\n",
-      "│   │   ├── dataset_description.json\r\n",
-      "│   │   ├── README\r\n",
-      "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n",
-      "│   │       └── \u001b[01;34mses-001\u001b[00m\r\n",
-      "│   │           └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n",
-      "│   │               └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n",
-      "│   └── \u001b[01;34msource\u001b[00m\r\n",
-      "│       ├── CHANGES\r\n",
-      "│       ├── dataset_description.json\r\n",
-      "│       ├── README\r\n",
-      "│       └── \u001b[01;34msub-001\u001b[00m\r\n",
-      "│           └── \u001b[01;34mses-001\u001b[00m\r\n",
-      "│               └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n",
-      "│                   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n",
-      "└── README.md\r\n",
+      "\u001b[01;34moutput\u001b[00m\r\n",
+      "└── \u001b[01;34msource\u001b[00m\r\n",
+      "    ├── dataset_description.json\r\n",
+      "    └── \u001b[01;34msub-001\u001b[00m\r\n",
+      "        └── \u001b[01;34mses-001\u001b[00m\r\n",
+      "            └── \u001b[01;34mfunc\u001b[00m\r\n",
       "\r\n",
-      "9 directories, 19 files\r\n",
+      "4 directories, 1 file\r\n",
       "\n"
      ]
     }
    ],
    "source": [
-    "!tree"
+    "!tree output"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 38,
    "metadata": {},
    "outputs": [
     {
@@ -162,42 +187,83 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 45,
    "metadata": {},
    "outputs": [],
    "source": [
     "cfg.mri.repetitionTime = 2.1;\n",
-    "cfg.mri.contrastEnhancement = [];\n",
-    "cfg.mri.phaseEncodingDirection = [];\n",
-    "cfg.mri.reconstruction = 'fast';\n",
-    "cfg.mri.echo = '1';\n",
-    "cfg.mri.acquisition = 'slow';"
+    "cfg.suffix.phaseEncodingDirection = 'i-';\n",
+    "cfg.suffix.reconstruction = 'motion correction';\n",
+    "cfg.suffix.echo = '1';\n",
+    "cfg.suffix.acquisition = 'slow';"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 48,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\r\n",
+      "\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "                                                   \r\n",
+      "         ___ ___ ___   ___ ___ ___  ___            \r\n",
+      "        / __| _ \\ _ \\ | _ )_ _|   \\/ __|\r\n",
+      "       | (__|  _/  _/ | _ \\| || |) \\__ \\\r\n",
+      "        \\___|_| |_|   |___/___|___/|___/\r\n",
+      "                                                   \r\n",
+      "Thank you for using the CPP BIDS - version v1.0.0. \r\n",
+      "\r\n",
+      "Current list of contributors includes:\r\n",
+      " Rémi Gau\r\n",
+      " Marco Barilari\r\n",
+      " Ceren Battal\r\n",
+      " Tomas Lenc\r\n",
+      "\b\r\n",
+      "\r\n",
+      "Please cite using the following DOI: \r\n",
+      " https://doi.org/10.5281/zenodo.4007674\r\n",
+      "\r\n",
+      "For bug report, suggestions or contributions see: \r\n",
+      " https://github.com/cpp-lln-lab/CPP_BIDS\r\n",
+      "\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "\r\n",
+      "\r\n",
+      "\r\n",
+      "Data will be saved in this directory:\r\n",
+      "\t/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func\r\n",
+      "\r\n",
+      "Data will be saved in this file:\r\n",
+      "\tsub-001_ses-001_task-testTask_run-001_events_date-202011171531.tsv\r\n"
+     ]
+    }
+   ],
    "source": [
     "[cfg] = createFilename(cfg);"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 47,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ans = sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.tsv\r\n"
+      "sub-001_ses-001_task-testTask_run-001_events_date-202011171531.tsv\r\n"
      ]
     }
    ],
    "source": [
-    "cfg.fileName.events"
+    "disp(cfg.fileName.events)"
    ]
   },
   {
@@ -213,65 +279,43 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 51,
    "metadata": {},
    "outputs": [],
    "source": [
-    "createBoldJson(cfg)"
+    "createJson(cfg, 'func')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 52,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[01;34m.\u001b[00m\r\n",
-      "├── basic_usage.ipynb\r\n",
-      "├── creating_BIDS_dataset.ipynb\r\n",
-      "├── more_on_saving.ipynb\r\n",
-      "├── octave-workspace\r\n",
-      "├── \u001b[01;34moutput\u001b[00m\r\n",
-      "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n",
-      "│   │   ├── CHANGES\r\n",
-      "│   │   ├── dataset_description.json\r\n",
-      "│   │   ├── README\r\n",
-      "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n",
-      "│   │       └── \u001b[01;34mses-001\u001b[00m\r\n",
-      "│   │           └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n",
-      "│   │               └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n",
-      "│   └── \u001b[01;34msource\u001b[00m\r\n",
-      "│       ├── CHANGES\r\n",
-      "│       ├── dataset_description.json\r\n",
-      "│       ├── README\r\n",
-      "│       └── \u001b[01;34msub-001\u001b[00m\r\n",
-      "│           └── \u001b[01;34mses-001\u001b[00m\r\n",
-      "│               └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008142237.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n",
-      "│                   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n",
-      "└── README.md\r\n",
+      "\u001b[01;34moutput\u001b[00m\r\n",
+      "└── \u001b[01;34msource\u001b[00m\r\n",
+      "    ├── dataset_description.json\r\n",
+      "    └── \u001b[01;34msub-001\u001b[00m\r\n",
+      "        └── \u001b[01;34mses-001\u001b[00m\r\n",
+      "            └── \u001b[01;34mfunc\u001b[00m\r\n",
+      "                ├── sub-001_ses-001_task-testTask_run-001_bold_date-202011171530.json\r\n",
+      "                └── sub-001_ses-001_task-testTask_run-001_bold_date-202011171531.json\r\n",
       "\r\n",
-      "9 directories, 20 files\r\n",
+      "4 directories, 3 files\r\n",
       "\n"
      ]
     }
    ],
    "source": [
-    "!tree"
+    "!tree output"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 44,
    "metadata": {},
    "outputs": [
     {
@@ -283,27 +327,6 @@
       "    \"RepetitionTime\": [],\r\n",
       "    \"SliceTiming\": [],\r\n",
       "    \"TaskDescription\": \"\",\r\n",
-      "    \"TaskName\": \"test Task\",\r\n",
-      "    \"timing\": {\r\n",
-      "        \"IBI\": 5.4,\r\n",
-      "        \"ISI\": 0.1,\r\n",
-      "        \"onsetDelay\": 0.1,\r\n",
-      "        \"endDelay\": 0.1,\r\n",
-      "        \"eventDuration\": 0.8\r\n",
-      "    },\r\n",
-      "    \"dot\": {\r\n",
-      "        \"speed\": 30,\r\n",
-      "        \"coherence\": 1,\r\n",
-      "        \"density\": 0.1,\r\n",
-      "        \"lifeTime\": 10,\r\n",
-      "        \"proportionKilledPerFrame\": 0,\r\n",
-      "        \"size\": 1\r\n",
-      "    }\r\n",
-      "}{\r\n",
-      "    \"Instructions\": \"\",\r\n",
-      "    \"RepetitionTime\": [],\r\n",
-      "    \"SliceTiming\": [],\r\n",
-      "    \"TaskDescription\": \"\",\r\n",
       "    \"TaskName\": \"test Task\"\r\n",
       "}\n"
      ]
@@ -326,7 +349,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -365,12 +388,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "createBoldJson(cfg, parameters)"
+    "createJson(cfg, parameters)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
@@ -382,43 +405,7 @@
       "    \"RepetitionTime\": [],\r\n",
       "    \"SliceTiming\": [],\r\n",
       "    \"TaskDescription\": \"\",\r\n",
-      "    \"TaskName\": \"test Task\",\r\n",
-      "    \"timing\": {\r\n",
-      "        \"IBI\": 5.4,\r\n",
-      "        \"ISI\": 0.1,\r\n",
-      "        \"onsetDelay\": 0.1,\r\n",
-      "        \"endDelay\": 0.1,\r\n",
-      "        \"eventDuration\": 0.8\r\n",
-      "    },\r\n",
-      "    \"dot\": {\r\n",
-      "        \"speed\": 30,\r\n",
-      "        \"coherence\": 1,\r\n",
-      "        \"density\": 0.1,\r\n",
-      "        \"lifeTime\": 10,\r\n",
-      "        \"proportionKilledPerFrame\": 0,\r\n",
-      "        \"size\": 1\r\n",
-      "    }\r\n",
-      "}{\r\n",
-      "    \"Instructions\": \"\",\r\n",
-      "    \"RepetitionTime\": [],\r\n",
-      "    \"SliceTiming\": [],\r\n",
-      "    \"TaskDescription\": \"\",\r\n",
-      "    \"TaskName\": \"test Task\",\r\n",
-      "    \"timing\": {\r\n",
-      "        \"IBI\": 5.4,\r\n",
-      "        \"ISI\": 0.1,\r\n",
-      "        \"onsetDelay\": 0.1,\r\n",
-      "        \"endDelay\": 0.1,\r\n",
-      "        \"eventDuration\": 0.8\r\n",
-      "    },\r\n",
-      "    \"dot\": {\r\n",
-      "        \"speed\": 30,\r\n",
-      "        \"coherence\": 1,\r\n",
-      "        \"density\": 0.1,\r\n",
-      "        \"lifeTime\": 10,\r\n",
-      "        \"proportionKilledPerFrame\": 0,\r\n",
-      "        \"size\": 1\r\n",
-      "    }\r\n",
+      "    \"TaskName\": \"test Task\"\r\n",
       "}\n"
      ]
     }
@@ -438,7 +425,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {
@@ -446,8 +433,17 @@
      "output_type": "stream",
      "text": [
       "onset\tduration\ttrial_type\ttarget_position\ttarget_type\n",
-      "2.000000\t1.000000\tmotion_up\tleft\taudio\t\n",
-      "6.000000\t1.200000\tstatic\tright\tvisual\t\n"
+      "ans =  2\n",
+      "2.000000\tans =  1\n",
+      "1.000000\tmotion_up\tleft\taudio\t\n",
+      "ans =  6\n",
+      "6.000000\tans =  1.2000\n",
+      "1.200000\tstatic\tright\tvisual\t\n",
+      "\n",
+      "Data were saved in this file:\n",
+      "\n",
+      "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202011171307.tsv\n",
+      "\n"
      ]
     }
    ],
@@ -455,6 +451,7 @@
     "\n",
     "logFile.extraColumns = {'target_position', 'target_type'};\n",
     "\n",
+    "logFile = saveEventsFile('init', cfg, logFile);\n",
     "logFile = saveEventsFile('open', cfg, logFile);\n",
     "\n",
     "logFile(1,1).onset = 2;\n",
@@ -476,7 +473,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 53,
    "metadata": {
     "scrolled": false
    },
@@ -485,46 +482,22 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[01;34m.\u001b[00m\r\n",
-      "├── basic_usage.ipynb\r\n",
-      "├── creating_BIDS_dataset.ipynb\r\n",
-      "├── more_on_saving.ipynb\r\n",
-      "├── octave-workspace\r\n",
-      "├── \u001b[01;34moutput\u001b[00m\r\n",
-      "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n",
-      "│   │   ├── CHANGES\r\n",
-      "│   │   ├── dataset_description.json\r\n",
-      "│   │   ├── README\r\n",
-      "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n",
-      "│   │       └── \u001b[01;34mses-001\u001b[00m\r\n",
-      "│   │           └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n",
-      "│   │               └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n",
-      "│   └── \u001b[01;34msource\u001b[00m\r\n",
-      "│       ├── CHANGES\r\n",
-      "│       ├── dataset_description.json\r\n",
-      "│       ├── README\r\n",
-      "│       └── \u001b[01;34msub-001\u001b[00m\r\n",
-      "│           └── \u001b[01;34mses-001\u001b[00m\r\n",
-      "│               └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008142237.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.tsv\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n",
-      "│                   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n",
-      "└── README.md\r\n",
+      "\u001b[01;34moutput\u001b[00m\r\n",
+      "└── \u001b[01;34msource\u001b[00m\r\n",
+      "    ├── dataset_description.json\r\n",
+      "    └── \u001b[01;34msub-001\u001b[00m\r\n",
+      "        └── \u001b[01;34mses-001\u001b[00m\r\n",
+      "            └── \u001b[01;34mfunc\u001b[00m\r\n",
+      "                ├── sub-001_ses-001_task-testTask_run-001_bold_date-202011171530.json\r\n",
+      "                └── sub-001_ses-001_task-testTask_run-001_bold_date-202011171531.json\r\n",
       "\r\n",
-      "9 directories, 22 files\r\n",
+      "4 directories, 3 files\r\n",
       "\n"
      ]
     }
    ],
    "source": [
-    "!tree"
+    "!tree output"
    ]
   },
   {
@@ -540,7 +513,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -549,7 +522,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [
     {
@@ -559,34 +532,17 @@
       "\u001b[01;34m.\u001b[00m\r\n",
       "├── basic_usage.ipynb\r\n",
       "├── creating_BIDS_dataset.ipynb\r\n",
-      "├── more_on_saving.ipynb\r\n",
-      "├── octave-workspace\r\n",
       "├── \u001b[01;34moutput\u001b[00m\r\n",
-      "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n",
+      "│   ├── \u001b[01;34mraw\u001b[00m\r\n",
       "│   │   ├── CHANGES\r\n",
       "│   │   ├── dataset_description.json\r\n",
       "│   │   ├── README\r\n",
-      "│   │   ├── \u001b[01;34msource\u001b[00m\r\n",
-      "│   │   │   ├── CHANGES\r\n",
-      "│   │   │   ├── dataset_description.json\r\n",
-      "│   │   │   ├── README\r\n",
-      "│   │   │   └── \u001b[01;34msub-001\u001b[00m\r\n",
-      "│   │   │       └── \u001b[01;34mses-001\u001b[00m\r\n",
-      "│   │   │           └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│   │   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n",
-      "│   │   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008142237.json\r\n",
-      "│   │   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n",
-      "│   │   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n",
-      "│   │   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.json\r\n",
-      "│   │   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.tsv\r\n",
-      "│   │   │               ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n",
-      "│   │   │               └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n",
       "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n",
       "│   │       └── \u001b[01;34mses-001\u001b[00m\r\n",
       "│   │           └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n",
-      "│   │               ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n",
-      "│   │               └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n",
+      "│   │               ├── sub-001_ses-001_task-testTask_run-001_bold.json\r\n",
+      "│   │               ├── sub-001_ses-001_task-testTask_run-001_events.json\r\n",
+      "│   │               └── sub-001_ses-001_task-testTask_run-001_events.tsv\r\n",
       "│   └── \u001b[01;34msource\u001b[00m\r\n",
       "│       ├── CHANGES\r\n",
       "│       ├── dataset_description.json\r\n",
@@ -594,17 +550,15 @@
       "│       └── \u001b[01;34msub-001\u001b[00m\r\n",
       "│           └── \u001b[01;34mses-001\u001b[00m\r\n",
       "│               └── \u001b[01;34mfunc\u001b[00m\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008142237.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.json\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.tsv\r\n",
-      "│                   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n",
-      "│                   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n",
-      "└── README.md\r\n",
+      "│                   ├── sub-001_ses-001_task-testTask_run-001_bold_date-202011171307.json\r\n",
+      "│                   ├── sub-001_ses-001_task-testTask_run-001_events_date-202011171307.json\r\n",
+      "│                   └── sub-001_ses-001_task-testTask_run-001_events_date-202011171307.tsv\r\n",
+      "├── README.md\r\n",
+      "├── saving_arrays.ipynb\r\n",
+      "├── saving_stim_files.ipynb\r\n",
+      "└── using_2_logfiles.ipynb\r\n",
       "\r\n",
-      "13 directories, 33 files\r\n",
+      "9 directories, 18 files\r\n",
       "\n"
      ]
     }
diff --git a/notebooks/demo_1_IoNS YRD_20201118.ipynb b/notebooks/demo_1_IoNS YRD_20201118.ipynb
new file mode 100644
index 00000000..97b94de0
--- /dev/null
+++ b/notebooks/demo_1_IoNS YRD_20201118.ipynb	
@@ -0,0 +1,179 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# CPP BIDS: quick demo 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% add the relevant functions from the source and library folder\n",
+    "addpath(genpath(fullfile(pwd, '..', 'src')))\n",
+    "addpath(genpath(fullfile(pwd, '..', 'lib')))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Simplest case: behavioral experiment"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Set up"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "% clean up\n",
+    "clear cfg logFile\n",
+    "rmdir(fullfile(pwd, 'new_experiment'), 's');\n",
+    "\n",
+    "% Define where to save things, subject and run number, task name\n",
+    "cfg.dir.output = fullfile(pwd, 'new_experiment');   \n",
+    "\n",
+    "cfg.subject.subjectNb = 1;\n",
+    "cfg.subject.runNb = 1;\n",
+    "\n",
+    "cfg.task.name = 'test task';\n",
+    "\n",
+    "% to print some output to the prompt\n",
+    "cfg.verbose = 1;\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Initialize the output files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cfg = createFilename(cfg);\n",
+    "logFile = saveEventsFile('init', cfg);\n",
+    "logFile = saveEventsFile('open', cfg, logFile);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Add content to the outpute file\n",
+    "\n",
+    "Append content to `logFile` and then save it."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "logFile(1, 1).onset = 2;\n",
+    "logFile(1, 1).trial_type = 'target';\n",
+    "logFile(1, 1).duration = 0.25;\n",
+    "\n",
+    "logFile(2, 1).onset = 5;\n",
+    "logFile(2, 1).trial_type = 'no_target';\n",
+    "logFile(2, 1).duration = 0.36;\n",
+    "\n",
+    "logFile = saveEventsFile('save', cfg, logFile);\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% close the file\n",
+    "saveEventsFile('close', cfg, logFile);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### check the output"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "!tree new_experiment"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!cat new_experiment/source/sub-001/ses-001/beh/sub-001_ses-001_task-testTask_run-001_events_date-*.tsv"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!cat new_experiment/source/sub-001/ses-001/beh/sub-001_ses-001_task-testTask_run-001_events_date-*.json"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Octave",
+   "language": "octave",
+   "name": "octave"
+  },
+  "language_info": {
+   "file_extension": ".m",
+   "help_links": [
+    {
+     "text": "GNU Octave",
+     "url": "https://www.gnu.org/software/octave/support.html"
+    },
+    {
+     "text": "Octave Kernel",
+     "url": "https://github.com/Calysto/octave_kernel"
+    },
+    {
+     "text": "MetaKernel Magics",
+     "url": "https://metakernel.readthedocs.io/en/latest/source/README.html"
+    }
+   ],
+   "mimetype": "text/x-octave",
+   "name": "octave",
+   "version": "4.2.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/notebooks/demo_2_IoNS YRD_20201118.ipynb b/notebooks/demo_2_IoNS YRD_20201118.ipynb
new file mode 100644
index 00000000..ee21c112
--- /dev/null
+++ b/notebooks/demo_2_IoNS YRD_20201118.ipynb	
@@ -0,0 +1,325 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# CPP BIDS: quick demo 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% add the relevant functions from the source and library folder\n",
+    "addpath(genpath(fullfile(pwd, '..', 'src')))\n",
+    "addpath(genpath(fullfile(pwd, '..', 'lib')))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# fMRI experiment with eyetracking"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Set up"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "% clean up\n",
+    "clear cfg logFile\n",
+    "\n",
+    "% Define where to save things, subject and run number, task name\n",
+    "cfg.dir.output = fullfile(pwd, 'new_experiment');    \n",
+    "\n",
+    "cfg.subject.subjectNb = 1;\n",
+    "cfg.subject.runNb = 1;\n",
+    "\n",
+    "cfg.task.name = 'test task';\n",
+    "\n",
+    "cfg.testingDevice = 'mri';\n",
+    "\n",
+    "cfg.eyeTracker.do = 1;\n",
+    "\n",
+    "% to print some output to the prompt\n",
+    "cfg.verbose = 1;\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Additional details about the experiment "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% other information to save in the TSV file\n",
+    "logFile.extraColumns = {'target_position', 'target_type'};\n",
+    "\n",
+    "% Time between events in seconds\n",
+    "parameters.timing.ISI = 0.1;\n",
+    "\n",
+    "% Number of seconds before the stimuli are presented\n",
+    "parameters.timing.onsetDelay = .1;\n",
+    "\n",
+    "% Event duration\n",
+    "parameters.timing.eventDuration = 0.8;\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## fMRI details"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cfg.mri.repetitionTime = 2.1;\n",
+    "\n",
+    "cfg.suffix.phaseEncodingDirection = 'AP';\n",
+    "cfg.suffix.reconstruction = 'MoCo';\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Initialize the output files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cfg = createFilename(cfg);\n",
+    "\n",
+    "logFile = saveEventsFile('init', cfg, logFile);\n",
+    "logFile = saveEventsFile('open', cfg, logFile);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Save metadata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "createJson(cfg, 'func', parameters)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!tree new_experiment"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add content to the outpute file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "logFile(1,1).onset = 2;\n",
+    "logFile(1,1).trial_type = 'motion_up';\n",
+    "logFile(1,1).duration = 1;\n",
+    "logFile(1,1).target_position = 'left';\n",
+    "logFile(1,1).target_type = 'audio';\n",
+    "\n",
+    "logFile(2,1).onset = 6;\n",
+    "logFile(2,1).trial_type = 'static';\n",
+    "logFile(2,1).duration = 1.2;\n",
+    "logFile(2,1).target_position = 'right';\n",
+    "logFile(2,1).target_type = 'visual';\n",
+    "\n",
+    "logFile = saveEventsFile('save', cfg, logFile);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% close the file\n",
+    "saveEventsFile('close', cfg, logFile);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Content of the `events.tsv` file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "!cat new_experiment/source/sub-001/ses-001/func/sub-001_ses-001_task-*events*.tsv"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Content of the data dictionary `events.json` file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!cat new_experiment/source/sub-001/ses-001/func/sub-001_ses-001_task-*events*.json"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Content of the metadata `bold.json` file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "!cat new_experiment/source/sub-001/ses-001/func/sub-001_ses-001_task-*bold*.json"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Convert to a BIDS dataset"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Create a dataset description"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "cfg.bids.datasetDescription.Name = 'A new BIDS dataset';\n",
+    "cfg.bids.datasetDescription.BIDSVersion =  '1.3';\n",
+    "cfg.bids.datasetDescription.License = 'CC-BY';\n",
+    "cfg.bids.datasetDescription.Authors = {'IONS YRD 2020'};\n",
+    "cfg.bids.datasetDescription.Acknowledgements = '';\n",
+    "cfg.bids.datasetDescription.HowToAcknowledge = '';\n",
+    "cfg.bids.datasetDescription.Funding = {''};\n",
+    "cfg.bids.datasetDescription.ReferencesAndLinks = {''};\n",
+    "cfg.bids.datasetDescription.DatasetDOI = '';\n",
+    "\n",
+    "[cfg] = createFilename(cfg);\n",
+    "createDatasetDescription(cfg)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "convertSourceToRaw(cfg)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!tree new_experiment"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Octave",
+   "language": "octave",
+   "name": "octave"
+  },
+  "language_info": {
+   "file_extension": ".m",
+   "help_links": [
+    {
+     "text": "GNU Octave",
+     "url": "https://www.gnu.org/software/octave/support.html"
+    },
+    {
+     "text": "Octave Kernel",
+     "url": "https://github.com/Calysto/octave_kernel"
+    },
+    {
+     "text": "MetaKernel Magics",
+     "url": "https://metakernel.readthedocs.io/en/latest/source/README.html"
+    }
+   ],
+   "mimetype": "text/x-octave",
+   "name": "octave",
+   "version": "4.2.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/notebooks/more_on_saving.ipynb b/notebooks/saving_arrays.ipynb
similarity index 76%
rename from notebooks/more_on_saving.ipynb
rename to notebooks/saving_arrays.ipynb
index b3c25aea..c3cb9fd0 100644
--- a/notebooks/more_on_saving.ipynb
+++ b/notebooks/saving_arrays.ipynb
@@ -4,17 +4,22 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Saving arrays in the tsv file"
+    "## Saving arrays in the tsv file\n",
+    "\n",
+    "It is possible to save several values at once in a tsv file."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
+    "clear cfg logFile\n",
+    "\n",
     "% add the relevant functions from the src folder\n",
-    "addpath(genpath(fullfile(pwd, '..', 'src')));\n",
+    "addpath(genpath(fullfile(pwd, '..', 'src')))\n",
+    "addpath(genpath(fullfile(pwd, '..', 'lib')))\n",
     "\n",
     "cfg.dir.output = fullfile(pwd, 'output');\n",
     "\n",
@@ -25,7 +30,7 @@
     "\n",
     "cfg.testingDevice = 'mri';\n",
     "\n",
-    "cfg.verbose = false;\n",
+    "cfg.verbose = 1;\n",
     "\n",
     "[cfg] = createFilename(cfg);\n",
     "\n",
@@ -41,24 +46,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "logFile.extraColumns.target_position.length =  2;\n",
-    "logFile.extraColumns.target_type.length =  1;"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Note that it is also possible to directly open the file: things will be intialised automatically."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 23,
    "metadata": {},
    "outputs": [
     {
@@ -70,6 +58,10 @@
     }
    ],
    "source": [
+    "logFile.extraColumns.target_position.length =  2;\n",
+    "logFile.extraColumns.target_type.length =  1;\n",
+    "\n",
+    "logFile = saveEventsFile('init', cfg, logFile);\n",
     "logFile = saveEventsFile('open', cfg, logFile);"
    ]
   },
@@ -82,7 +74,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 18,
    "metadata": {
     "scrolled": true
    },
@@ -91,7 +83,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2.000000\t1.000000\tmotion_up\tn/a\tn/a\tn/a\t2.000000\t1.000000\tvisual\t\r\n"
+      "ans =  2\r\n",
+      "ans =  1\r\n",
+      "ans =  2\r\n",
+      "ans =  1\r\n",
+      "\r\n",
+      "ans =  4\r\n",
+      "ans =  1\r\n",
+      "ans =  2\r\n",
+      "ans =  1\r\n",
+      "\r\n"
      ]
     }
    ],
@@ -99,16 +100,16 @@
     "% Trial one : missing duration value\n",
     "logFile(1,1).onset = 2;\n",
     "logFile(1,1).trial_type = 'motion_up';\n",
-    "logFile(1,1).duration = [];\n",
+    "logFile(1,1).duration = 1;\n",
     "logFile(1,1).target_position = [2, 1];\n",
     "logFile(1,1).target_type = 'visual';\n",
     "\n",
     "% Trial two\n",
-    "logFile(1,1).onset = 2;\n",
-    "logFile(1,1).trial_type = 'motion_up';\n",
-    "logFile(1,1).duration = 1;\n",
-    "logFile(1,1).target_position = [2, 1];\n",
-    "logFile(1,1).target_type = 'visual';\n",
+    "logFile(2,1).onset = 4;\n",
+    "logFile(2,1).trial_type = 'motion_up';\n",
+    "logFile(2,1).duration = 1;\n",
+    "logFile(2,1).target_position = [2, 1];\n",
+    "logFile(2,1).target_type = 'visual';\n",
     "\n",
     "logFile = saveEventsFile('save', cfg, logFile);"
    ]
@@ -122,7 +123,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
@@ -131,11 +132,14 @@
      "text": [
       "warning: Missing some target_position data for this event.\r\n",
       "warning: called from\r\n",
-      "    saveEventsFile>checkExtracolumns at line 219 column 13\r\n",
-      "    saveEventsFile>checklLogFile at line 140 column 21\r\n",
-      "    saveEventsFile>saveToLogFile at line 282 column 17\r\n",
-      "    saveEventsFile at line 90 column 21\r\n",
-      "6.000000\t1.200000\tstatic\tn/a\tn/a\tn/a\t3.000000\tn/a\taudio\t\r\n"
+      "    saveEventsFile>checkExtracolumns at line 288 column 13\r\n",
+      "    saveEventsFile>checklLogFile at line 173 column 21\r\n",
+      "    saveEventsFile>saveToLogFile at line 351 column 17\r\n",
+      "    saveEventsFile at line 123 column 21\r\n",
+      "ans =  6\r\n",
+      "ans =  1.2000\r\n",
+      "ans =  3\r\n",
+      "\r\n"
      ]
     }
    ],
@@ -159,7 +163,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [
     {
@@ -168,12 +172,16 @@
      "text": [
       "warning: A field for this event is longer than expected. Truncating the extra values.\r\n",
       "warning: called from\r\n",
-      "    saveEventsFile>nanPadding at line 269 column 9\r\n",
-      "    saveEventsFile>checkExtracolumns at line 214 column 14\r\n",
-      "    saveEventsFile>checklLogFile at line 140 column 21\r\n",
-      "    saveEventsFile>saveToLogFile at line 282 column 17\r\n",
-      "    saveEventsFile at line 90 column 21\r\n",
-      "6.000000\t1.200000\tstatic\tn/a\tn/a\tn/a\t3.000000\t4.000000\ttouch\t\r\n"
+      "    saveEventsFile>nanPadding at line 338 column 9\r\n",
+      "    saveEventsFile>checkExtracolumns at line 283 column 14\r\n",
+      "    saveEventsFile>checklLogFile at line 173 column 21\r\n",
+      "    saveEventsFile>saveToLogFile at line 351 column 17\r\n",
+      "    saveEventsFile at line 123 column 21\r\n",
+      "ans =  6\r\n",
+      "ans =  1.2000\r\n",
+      "ans =  3\r\n",
+      "ans =  4\r\n",
+      "\r\n"
      ]
     }
    ],
@@ -190,7 +198,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [
     {
@@ -200,7 +208,7 @@
       "\r\n",
       "Data were saved in this file:\r\n",
       "\r\n",
-      "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202008142241.tsv\r\n",
+      "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202011171253.tsv\r\n",
       "\r\n"
      ]
     }
@@ -222,7 +230,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 22,
    "metadata": {},
    "outputs": [
     {
@@ -245,15 +253,9 @@
     "logFile.extraColumns.Speed.length = 12;\n",
     "\n",
     "% open the file\n",
+    "logFile = saveEventsFile('init', cfg, logFile);\n",
     "logFile = saveEventsFile('open', cfg, logFile);\n"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Saving `_stim.tsv` files"
-   ]
   }
  ],
  "metadata": {
diff --git a/notebooks/saving_stim_files.ipynb b/notebooks/saving_stim_files.ipynb
new file mode 100644
index 00000000..ab95868a
--- /dev/null
+++ b/notebooks/saving_stim_files.ipynb
@@ -0,0 +1,287 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Saving `_stim.tsv` files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% add the relevant functions from the source and library folder\n",
+    "addpath(genpath(fullfile(pwd, '..', 'src')))\n",
+    "addpath(genpath(fullfile(pwd, '..', 'lib')))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Set Up"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\r\n",
+      "\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "                                                   \r\n",
+      "         ___ ___ ___   ___ ___ ___  ___            \r\n",
+      "        / __| _ \\ _ \\ | _ )_ _|   \\/ __|\r\n",
+      "       | (__|  _/  _/ | _ \\| || |) \\__ \\\r\n",
+      "        \\___|_| |_|   |___/___|___/|___/\r\n",
+      "                                                   \r\n",
+      "Thank you for using the CPP BIDS - version v2.0.0. \r\n",
+      "\r\n",
+      "Current list of contributors includes:\r\n",
+      " Remi Gau\r\n",
+      " Marco Barilari\r\n",
+      " Ceren Battal\r\n",
+      " Tomas Lenc\r\n",
+      "\b\r\n",
+      "\r\n",
+      "Please cite using the following DOI: \r\n",
+      " https://doi.org/10.5281/zenodo.4007674\r\n",
+      "\r\n",
+      "For bug report, suggestions or contributions see: \r\n",
+      " https://github.com/cpp-lln-lab/CPP_BIDS\r\n",
+      "\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "\r\n",
+      "\r\n",
+      "\r\n",
+      "Data will be saved in this directory:\r\n",
+      "\t/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func\r\n",
+      "\r\n",
+      "Data will be saved in this file:\r\n",
+      "\tsub-001_ses-001_task-testTask_run-001_events_date-202012250913.tsv\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "cfg.dir.output = fullfile(pwd, 'output');\n",
+    "\n",
+    "cfg.verbose = 2;\n",
+    "\n",
+    "cfg.subject.subjectNb = 1;\n",
+    "cfg.subject.runNb = 1;\n",
+    "\n",
+    "cfg.task.name = 'test task';\n",
+    "\n",
+    "cfg.testingDevice = 'mri';\n",
+    "\n",
+    "cfg = createFilename(cfg);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Define the columns of the stim.tsv"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "logFile.extraColumns = {'Speed', 'LHL24', 'is_Fixation'};\n",
+    "\n",
+    "logFile = saveEventsFile('init_stim', cfg, logFile);\n",
+    "\n",
+    "logFile.extraColumns.Speed.length = 1;\n",
+    "logFile.extraColumns.LHL24.length = 3;\n",
+    "logFile.extraColumns.is_Fixation.length = 1;"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "  scalar structure containing the fields:\n",
+      "\n",
+      "    extraColumns =\n",
+      "\n",
+      "      scalar structure containing the fields:\n",
+      "\n",
+      "        Speed =\n",
+      "\n",
+      "          scalar structure containing the fields:\n",
+      "\n",
+      "            bids: 1x1 scalar struct\n",
+      "            length: 1x1 scalar\n",
+      "\n",
+      "        LHL24 =\n",
+      "\n",
+      "          scalar structure containing the fields:\n",
+      "\n",
+      "            bids: 1x1 scalar struct\n",
+      "            length: 1x1 scalar\n",
+      "\n",
+      "        is_Fixation =\n",
+      "\n",
+      "          scalar structure containing the fields:\n",
+      "\n",
+      "            bids: 1x1 scalar struct\n",
+      "            length: 1x1 scalar\n",
+      "\n",
+      "\n",
+      "    onset =  55\n",
+      "    trial_type = motion_up\n",
+      "    duration =  66\n",
+      "    isStim = 1\n",
+      "    filename = sub-001_ses-001_task-testTask_run-001_stim_date-202012250913.tsv\n",
+      "    fileID =  3\n",
+      "    Speed =  2\n",
+      "    LHL24 =\n",
+      "\n",
+      "       1   2   3\n",
+      "\n",
+      "    is_Fixation = 1\n",
+      "\n",
+      "  scalar structure containing the fields:\n",
+      "\n",
+      "    extraColumns =\n",
+      "\n",
+      "      scalar structure containing the fields:\n",
+      "\n",
+      "        Speed =\n",
+      "\n",
+      "          scalar structure containing the fields:\n",
+      "\n",
+      "            bids: 1x1 scalar struct\n",
+      "            length: 1x1 scalar\n",
+      "\n",
+      "        LHL24 =\n",
+      "\n",
+      "          scalar structure containing the fields:\n",
+      "\n",
+      "            bids: 1x1 scalar struct\n",
+      "            length: 1x1 scalar\n",
+      "\n",
+      "        is_Fixation =\n",
+      "\n",
+      "          scalar structure containing the fields:\n",
+      "\n",
+      "            bids: 1x1 scalar struct\n",
+      "            length: 1x1 scalar\n",
+      "\n",
+      "\n",
+      "    onset =  55\n",
+      "    trial_type = motion_up\n",
+      "    duration =  66\n",
+      "    isStim = 1\n",
+      "    filename = sub-001_ses-001_task-testTask_run-001_stim_date-202012250913.tsv\n",
+      "    fileID =  3\n",
+      "    Speed =  2\n",
+      "    LHL24 =\n",
+      "\n",
+      "       1   2   3\n",
+      "\n",
+      "    is_Fixation = 1\n",
+      "2.000000\t1.000000\t2.000000\t3.000000\ttrue\t\n",
+      "\n",
+      "Data were saved in this file:\n",
+      "\n",
+      "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_stim_date-202012250913.tsv\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "% create the events file and header\n",
+    "logFile = saveEventsFile('open', cfg, logFile);\n",
+    "\n",
+    "% ROW 1\n",
+    "logFile(1, 1).onset = 55;\n",
+    "logFile(end, 1).trial_type = 'motion_up';\n",
+    "logFile(end, 1).duration = 66;\n",
+    "logFile(end, 1).Speed = 2;\n",
+    "logFile(end, 1).LHL24 = 1:3;\n",
+    "logFile(end, 1).is_Fixation = true;\n",
+    "\n",
+    "logFile = saveEventsFile('save', cfg, logFile);\n",
+    "\n",
+    "% close the file\n",
+    "saveEventsFile('close', cfg, logFile);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Inspect the content of the stim.tsv file\n",
+    "    \n",
+    "The `onset`, `duration` and `trial_type` are ignored because they were note spcified in the `extraColumns` field.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "2.000000\t1.000000\t2.000000\t3.000000\ttrue\t\r\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "!cat output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_stim_date-*.tsv "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Octave",
+   "language": "octave",
+   "name": "octave"
+  },
+  "language_info": {
+   "file_extension": ".m",
+   "help_links": [
+    {
+     "text": "GNU Octave",
+     "url": "https://www.gnu.org/software/octave/support.html"
+    },
+    {
+     "text": "Octave Kernel",
+     "url": "https://github.com/Calysto/octave_kernel"
+    },
+    {
+     "text": "MetaKernel Magics",
+     "url": "https://metakernel.readthedocs.io/en/latest/source/README.html"
+    }
+   ],
+   "mimetype": "text/x-octave",
+   "name": "octave",
+   "version": "4.2.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/notebooks/using_2_logfiles.ipynb b/notebooks/using_2_logfiles.ipynb
new file mode 100644
index 00000000..ef29eddb
--- /dev/null
+++ b/notebooks/using_2_logfiles.ipynb
@@ -0,0 +1,256 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Saving two `_events.tsv` for the same run\n",
+    "\n",
+    "This won't create BIDS valid output but this might help you organize some of your output in different TSV files.\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% add the relevant functions from the src folder\n",
+    "addpath(genpath(fullfile(pwd, '..', 'src')))\n",
+    "addpath(genpath(fullfile(pwd, '..', 'lib')))\n",
+    "\n",
+    "cfg.dir.output = fullfile(pwd, 'output');\n",
+    "\n",
+    "cfg.task.name = 'test task';\n",
+    "\n",
+    "cfg.subject.subjectNb = 1;\n",
+    "cfg.subject.runNb = 1;"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## create a first logfile"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\r\n",
+      "\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "                                                   \r\n",
+      "         ___ ___ ___   ___ ___ ___  ___            \r\n",
+      "        / __| _ \\ _ \\ | _ )_ _|   \\/ __|\r\n",
+      "       | (__|  _/  _/ | _ \\| || |) \\__ \\\r\n",
+      "        \\___|_| |_|   |___/___|___/|___/\r\n",
+      "                                                   \r\n",
+      "Thank you for using the CPP BIDS - version v1.0.0. \r\n",
+      "\r\n",
+      "Current list of contributors includes:\r\n",
+      " Rémi Gau\r\n",
+      " Marco Barilari\r\n",
+      " Ceren Battal\r\n",
+      " Tomas Lenc\r\n",
+      "\b\r\n",
+      "\r\n",
+      "Please cite using the following DOI: \r\n",
+      " https://doi.org/10.5281/zenodo.4007674\r\n",
+      "\r\n",
+      "For bug report, suggestions or contributions see: \r\n",
+      " https://github.com/cpp-lln-lab/CPP_BIDS\r\n",
+      "\r\n",
+      "___________________________________________________\r\n",
+      "___________________________________________________\r\n",
+      "\r\n",
+      "\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "[cfg] = createFilename(cfg);\n",
+    "logFile.extraColumns = {'target_position', 'target_type'};"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "onset\tduration\ttrial_type\ttarget_position\ttarget_type\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "logFile = saveEventsFile('init', cfg, logFile);\n",
+    "logFile = saveEventsFile('open', cfg, logFile);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## create a second logfile"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "% we use a copy of the configuration and we modify the 'acq' field in the BIDS naming convention\n",
+    "cfg_2 = cfg;\n",
+    "cfg_2.suffix.acquisition = 'extraInfo';\n",
+    "\n",
+    "[cfg_2] = createFilename(cfg_2);\n",
+    "logFile_2.extraColumns = {'target_color'};"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "onset\tduration\ttrial_type\ttarget_color\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "logFile_2 = saveEventsFile('init', cfg_2, logFile_2);\n",
+    "logFile_2 = saveEventsFile('open', cfg_2, logFile_2);\n",
+    "clear cfg2 % we don't need it anymore as this was only need to create the new filename"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## log file into the 2 different files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "ans =  2\n",
+      "ans =  0.50000\n",
+      "ans =  2\n",
+      "\n",
+      "ans =  3\n",
+      "ans =  1\n",
+      "ans =  1\n",
+      "\n",
+      "\n",
+      "\n",
+      "ans =  2\n",
+      "ans =  0.50000\n",
+      "\n",
+      "ans =  3\n",
+      "ans =  1\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "% Trial one\n",
+    "logFile(1,1).onset = 2;\n",
+    "logFile(1,1).trial_type = 'motion_up';\n",
+    "logFile(1,1).duration = 0.5;\n",
+    "logFile(1,1).target_position = 2;\n",
+    "logFile(1,1).target_type = 'visual';\n",
+    "\n",
+    "% we do have to repeat some information here for onset, duration, trial type\n",
+    "logFile_2(1,1).onset = 2;\n",
+    "logFile_2(1,1).trial_type = 'motion_up';\n",
+    "logFile_2(1,1).duration = 0.5;\n",
+    "logFile_2(1,1).target_color = 'red';\n",
+    "\n",
+    "% Trial two\n",
+    "logFile(2,1).onset = 3;\n",
+    "logFile(2,1).trial_type = 'motion_down';\n",
+    "logFile(2,1).duration = 1;\n",
+    "logFile(2,1).target_position = 1;\n",
+    "logFile(2,1).target_type = 'visual';\n",
+    "\n",
+    "logFile_2(2,1).onset = 3;\n",
+    "logFile_2(2,1).trial_type = 'motion_down';\n",
+    "logFile_2(2,1).duration = 1;\n",
+    "logFile_2(2,1).target_color = 'blue';\n",
+    "\n",
+    "% save to the tsv file\n",
+    "logFile = saveEventsFile('save', cfg, logFile);\n",
+    "\n",
+    "% skip lines for display\n",
+    "fprintf(1, '\\n\\n')\n",
+    "\n",
+    "logFile_2 = saveEventsFile('save', cfg, logFile_2);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saveEventsFile('close', cfg, logFile);\n",
+    "saveEventsFile('close', cfg, logFile_2);"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Octave",
+   "language": "octave",
+   "name": "octave"
+  },
+  "language_info": {
+   "file_extension": ".m",
+   "help_links": [
+    {
+     "text": "GNU Octave",
+     "url": "https://www.gnu.org/software/octave/support.html"
+    },
+    {
+     "text": "Octave Kernel",
+     "url": "https://github.com/Calysto/octave_kernel"
+    },
+    {
+     "text": "MetaKernel Magics",
+     "url": "https://metakernel.readthedocs.io/en/latest/source/README.html"
+    }
+   ],
+   "mimetype": "text/x-octave",
+   "name": "octave",
+   "version": "4.2.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..471b6d23
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,7 @@
+Sphinx
+sphinxcontrib-matlabdomain
+sphinxcontrib-napoleon
+sphinx_rtd_theme
+miss_hit==0.9.15
+notebook
+octave_kernel
\ No newline at end of file
diff --git a/src/checkCFG.m b/src/checkCFG.m
index df2a69a8..07636767 100644
--- a/src/checkCFG.m
+++ b/src/checkCFG.m
@@ -1,10 +1,186 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function cfg = checkCFG(cfg)
-    % cfg = checkCFG(cfg)
     %
-    % check that we have all the fields that we need in the experiment parameters
-    % reuses a lot of code from the BIDS starter kit
+    % Check the fields of the configuration structure ``cfg``. If a required field is
+    % missing the default value will be assigned to that field. If this field already
+    % exists then the existing value will not be replaced.
+    %
+    % USAGE::
+    %
+    %   cfg = checkCFG([cfg])
+    %
+    % :param cfg: The configuration variable to check.
+    % :type cfg: structure
+    %
+    % :returns: :cfg: (structure)
+    %
+    % This function reuses a lot of code and comment from the BIDS starter kit:
+    %
+    % https://github.com/bids-standard/bids-starter-kit/tree/master/matlabCode
+    %
+    % **Fields descriptions**:
+    %  The following section describes the main fields set by ``checkCFG()`` with
+    %  their associated default value.
+    %
+    %   - ``cfg.testingDevice = 'pc'``
+    %     sets the way the experiment is run and the different options match the imaging
+    %     modality:
+    %
+    %     - ``pc`` is for behavioral test
+    %     - ``mri`` is for fMRI
+    %     - ``eeg`` is for EEG...
+    %
+    %   - ``cfg.verbose = 0``
+    %     sets how talkative the code will be. Possible values range from ``0`` to ``2``.
+    %
+    %     - ``0``: "I don't want to hear anything from CPP_BIDS."
+    %     - ``1``: "I want to get my warnings."
+    %     - ``2``: "Tell me everything!"
+    %
+    %     For implementation see ``utils/talkToMe`` and ``utils/throwWarning``.
+    %
+    %   - ``cfg.useGUI = false``
+    %     sets whether a graphic interface should be used for the ``userInputs()``
+    %     to query about group name, as well as for session, subject and run number.
+    %
+    %   - ``cfg.dir.output``
+    %     sets where the data will be saved.
+    %
+    %   Filename options:
+    %     sets options that will help in creating the filenames.
+    %
+    %     - ``cfg.fileName.task = ''``
+    %       sets the name to be given to the task
+    %     - ``cfg.fileName.zeroPadding = 3``
+    %       sets tha amount of 0 padding the subject, session and run number.
+    %     - ``cfg.fileName.dateFormat = 'yyyymmddHHMM'``
+    %       sets the format of the date and time stamp that will be appended to all files.
+    %
+    %     The following fields can be used to specify certain of the labels that are used
+    %     to specify certain of the acquisition conditions of certain experemental runs
+    %     in a BIDS data set. These are mostly for MRI and, if set, will be ignored
+    %     for most other modalities. See ``tests/test_createFilename()`` for details on how
+    %     to use these.
+    %
+    %     - ``cfg.suffix.contrastEnhancement = []``
+    %     - ``cfg.suffix.phaseEncodingDirection = []``
+    %     - ``cfg.suffix.reconstruction = []``
+    %     - ``cfg.suffix.echo = []``
+    %     - ``cfg.suffix.acquisition = []``
+    %     - ``cfg.suffix.recording = []``
+    %
+    %   Group and session options:
+    %     All the fields of ``cfg.subject`` can be set using the ``userInputs()`` function
+    %     but can also be set "manually" directly into the ``cfg`` structure.
+    %
+    %     - ``cfg.subject.subjectGrp = ''``
+    %       is set to empty in case no group was provided.
+    %     - ``cfg.subject.sessionNb = 1``
+    %       always sets to 1 in case no session was provided.
+    %     - ``cfg.subject.askGrpSess = [true true]``
+    %       means that ``userInputs()`` will always ask for group and session by default.
+    %
+    %   Eyetracker options:
+    %     Those options are mostly work in progress at the moment but should allow to
+    %     track the some of the metadata regarding eyetracking data acquisition.
+    %
+    %     - ``cfg.eyeTracker.do = false``
+    %     - ``cfg.eyeTracker.SamplingFrequency = []``
+    %     - ``cfg.eyeTracker.PupilPositionType = ''``
+    %     - ``cfg.eyeTracker.RawSamples =  []``
+    %     - ``cfg.eyeTracker.Manufacturer = ''``
+    %     - ``cfg.eyeTracker.ManufacturersModelName = ''``
+    %     - ``cfg.eyeTracker.SoftwareVersions = ''``
+    %     - ``cfg.eyeTracker.CalibrationType = 'HV5'``
+    %     - ``cfg.eyeTracker.CalibrationPosition = ''``
+    %     - ``cfg.eyeTracker.CalibrationDistance = ''``
+    %     - ``cfg.eyeTracker.MaximalCalibrationError = []``
+    %     - ``cfg.eyeTracker.AverageCalibrationError = []``
+    %     - ``cfg.eyeTracker.RawDataFilters = {}``
+    %
+    % ``cfg.bids``:
+    %  ``checkCFG()`` will also initialize ``cfg.bids`` that
+    %  contains any information related to a BIDS data set and that will end up in
+    %  in one of the JSON "sidecar" files containing the metadata of your
+    %  experiment.
+    %
+    %  If the content of some fields of ``cfg`` has been set before running ``checkCFG()``,
+    %  that content might be copied into the relevant field in ``cfg.bids``. For example,
+    %  if you have set the field ``cfg.mri.repetitionTime``, then when you run ``checkCFG()``,
+    %  its content will also be copied into ``cfg.bids.mri.RepetitionTime``.
+    %
+    %  ``cfg.bids`` is further sub-divided into several fields for the different
+    %  "imaging modalities".
+    %
+    %  - ``cfg.bids.datasetDescription`` will be there for all type of experiments
+    %  - ``cfg.bids.beh`` is for purely behavioral experiment with no associated imaging
+    %  - ``cfg.bids.mri`` is for fMRI experiments
+    %  - ``cfg.bids.eeg`` is for EEG experiments
+    %  - ``cfg.bids.meg`` is for MEG experiments
+    %  - ``cfg.bids.ieeg`` is for iEEG experiments
+    %
+    %  The content of each of those subfields matches the different "keys" one can find
+    %  in the JSON file for each modality. The content of those different keys is detailed
+    %  in the code of ``checkCFG()``,
+    %  but a more extensive and updated descriptions will be found in the
+    %  BIDS specifications themselves.
+    %
+    %  https://bids-specification.readthedocs.io/en/stable/
+    %
+    %  For the content of the ``datasetDescription.json`` files::
+    %
+    %    cfg.bids.datasetDescription.Name = '';
+    %    cfg.bids.datasetDescription.BIDSVersion =  '';
+    %    cfg.bids.datasetDescription.License = '';
+    %    cfg.bids.datasetDescription.Authors = {''};
+    %    cfg.bids.datasetDescription.Acknowledgements = '';
+    %    cfg.bids.datasetDescription.HowToAcknowledge = '';
+    %    cfg.bids.datasetDescription.Funding = {''};
+    %    cfg.bids.datasetDescription.ReferencesAndLinks = {''};
+    %    cfg.bids.datasetDescription.DatasetDOI = '';
+    %
+    %  For the content of the JSON files for behavioral data::
+    %
+    %    cfg.bids.beh.TaskName = [];
+    %    cfg.bids.beh.Instructions = [];
+    %
+    %  For the content of the JSON files for fMRI data::
+    %
+    %    cfg.bids.mri.TaskName = '';
+    %    cfg.bids.mri.Instructions = '';
+    %    cfg.bids.mri.RepetitionTime = [];
+    %    cfg.bids.mri.SliceTiming = '';
+    %    cfg.bids.mri.TaskDescription = '';
+    %
+    %  For the content of the JSON files for EEG::
+    %
+    %    cfg.bids.eeg.TaskName = '';
+    %    cfg.bids.eeg.Instructions = '';
+    %    cfg.bids.eeg.EEGReference = '';
+    %    cfg.bids.eeg.SamplingFrequency = [];
+    %    cfg.bids.eeg.PowerLineFrequency = 50;
+    %    cfg.bids.eeg.SoftwareFilters = 'n/a';
+    %
+    %  For the content of the JSON files for iEEG::
+    %
+    %    cfg.bids.ieeg.TaskName = '';
+    %    cfg.bids.ieeg.Instructions = '';
+    %    cfg.bids.ieeg.iEEGReference = '';
+    %    cfg.bids.ieeg.SamplingFrequency = [];
+    %    cfg.bids.ieeg.PowerLineFrequency = 50;
+    %    cfg.bids.ieeg.SoftwareFilters = 'n/a';
+    %
+    %  For the content of the JSON files for MEG::
+    %
+    %    cfg.bids.meg.TaskName = '';
+    %    cfg.bids.meg.Instructions = '';
+    %    cfg.bids.meg.SamplingFrequency = [];
+    %    cfg.bids.meg.PowerLineFrequency = [];
+    %    cfg.bids.meg.DewarPosition = [];
+    %    cfg.bids.meg.SoftwareFilters = [];
+    %    cfg.bids.meg.DigitizedLandmarks = [];
+    %    cfg.bids.meg.DigitizedHeadPoints = [];
 
     if nargin < 1 || isempty(cfg)
         cfg = struct();
@@ -12,8 +188,6 @@
 
     checkCppBidsDependencies(cfg);
 
-    %% list the defaults to set
-
     fieldsToSet.verbose = 0;
 
     fieldsToSet.useGUI = false;
@@ -39,12 +213,12 @@
 
     %% BIDS
 
-    fieldsToSet = behJsonDefaults(fieldsToSet);
     fieldsToSet = datasetDescriptionDefaults(fieldsToSet);
+    fieldsToSet = behJsonDefaults(fieldsToSet);
+    fieldsToSet = mriJsonDefaults(fieldsToSet);
     fieldsToSet = eegJsonDefaults(fieldsToSet);
     fieldsToSet = ieegJsonDefaults(fieldsToSet);
     fieldsToSet = megJsonDefaults(fieldsToSet);
-    fieldsToSet = mriJsonDefaults(fieldsToSet);
 
     fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
 
@@ -61,7 +235,6 @@
     fieldsToSet.suffix.reconstruction = [];
     fieldsToSet.suffix.echo = [];
     fieldsToSet.suffix.acquisition = [];
-    fieldsToSet.suffix.repetitionTime = [];
     fieldsToSet.suffix.recording = [];
 
     fieldsToSet.suffix = orderfields(fieldsToSet.suffix);
@@ -111,6 +284,17 @@
 
 end
 
+function fieldsToSet = behJsonDefaults(fieldsToSet)
+    % for json for BEH data
+
+    fieldsToSet.bids.beh.TaskName = [];
+
+    fieldsToSet.bids.beh.Instructions = [];
+
+    fieldsToSet.bids.beh = orderfields(fieldsToSet.bids.beh);
+
+end
+
 function fieldsToSet = mriJsonDefaults(fieldsToSet)
     % for json for funcfional MRI data
 
@@ -176,7 +360,7 @@
 
     % REQUIRED Position of the dewar during the MEG scan: "upright", "supine" or
     % "degrees" of angle from vertical: for example on CTF systems,
-    % upright=15°, supine = 90°:
+    % upright=15 deg, supine = 90 deg:
     fieldsToSet.bids.meg.DewarPosition = [];
 
     % REQUIRED List of temporal and/or spatial software filters applied, or ideally
@@ -236,17 +420,6 @@
 
 end
 
-function fieldsToSet = behJsonDefaults(fieldsToSet)
-    % for json for BEH data
-
-    fieldsToSet.bids.beh.TaskName = [];
-
-    fieldsToSet.bids.beh.Instructions = [];
-
-    fieldsToSet.bids.ieeg = orderfields(fieldsToSet.bids.beh);
-
-end
-
 function fieldsToSet = eyetrackerDefaults(fieldsToSet)
 
     fieldsToSet.eyeTracker.do = false;
diff --git a/src/convertSourceToRaw.m b/src/convertSourceToRaw.m
index f4b4ea4f..edb6dcaf 100644
--- a/src/convertSourceToRaw.m
+++ b/src/convertSourceToRaw.m
@@ -1,15 +1,23 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function convertSourceToRaw(cfg)
-    % convertSourceToRaw(cfg)
     %
-    % attempts to convert a source dataset created with CPP_BIDS into a valid
+    % Function attempts to convert a source dataset created with CPP_BIDS into a valid
     % BIDS data set.
-    % - creates dummy README and CHANGE file
-    % - copy source dir to raw dir
-    % - remove the date suffix (_date-YYYYMMDDHHMM) from the files where it is present
     %
-    % Only covers func folder at the moment
+    %
+    % USAGE::
+    %
+    %   convertSourceToRaw(cfg)
+    %
+    % :param cfg: cfg structure is needed only for providing the path in ``cfg.dir.output``.
+    % :type cfg: structure
+    %
+    % :output:
+    %          - :creates: a dummy README and CHANGE file
+    %          - :copies: ``source`` directory to ``raw`` directory
+    %          - :removes: the date suffix ``_date-*`` from the files where it is present
+    %          - :zips: the ``_stim.tsv`` files.
 
     sourceDir = fullfile(cfg.dir.output, 'source');
     rawDir = fullfile(cfg.dir.output, 'raw');
diff --git a/src/createDataDictionary.m b/src/createDataDictionary.m
index 62639f0d..28d8d560 100644
--- a/src/createDataDictionary.m
+++ b/src/createDataDictionary.m
@@ -1,32 +1,55 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function createDataDictionary(cfg, logFile)
-    % createDataDictionary(cfg, logFile)
     %
-    % creates the data dictionary to be associated with a _events.tsv file
-    % will create empty field that you can then fill in manually in the JSON
-    % file
+    % It creates the data dictionary to be associated with a _events.tsv file. It will create empty
+    % fields that you can then fill in manually in the JSON file.
+    %
+    % USAGE::
+    %
+    %   createDataDictionary(cfg, logFile)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    % :param logFile: Contains the data you want to save.
+    % :type logFile: structure
+
+    fileName = strrep(logFile(1).filename, '.tsv', '.json');
+    fullFilename = getFullFilename(fileName, cfg);
+
+    jsonContent = setJsonContent(logFile);
 
     opts.Indent = '    ';
 
-    fileName = strrep(logFile(1).filename, '.tsv', '.json');
+    bids.util.jsonencode(fullFilename, jsonContent, opts);
+
+end
+
+function jsonContent = setJsonContent(logFile)
 
-    fileName = fullfile( ...
-                        cfg.dir.outputSubject, ...
-                        cfg.fileName.modality, ...
-                        fileName);
-
-    jsonContent = struct( ...
-                         'onset', struct( ...
-                                         'Description', 'time elapsed since experiment start', ...
-                                         'Unit', 's'), ...
-                         'trial_type', struct( ...
-                                              'Description', 'types of trial', ...
-                                              'Levels', ''), ...
-                         'duration', struct( ...
-                                            'Description', 'duration of the event or the block', ...
-                                            'Unit', 's') ...
-                        );
+    % regular _events file: add default _event file fields to the json content
+    if ~isfield(logFile, 'isStim') || isempty(logFile.isStim) || ~logFile.isStim
+
+        jsonContent = logFile.columns;
+
+        % _stim file: write stim-specific fields to the json content
+    elseif logFile.isStim
+
+        samplingFrequency = nan;
+        startTime = nan;
+
+        if isfield(logFile, 'SamplingFrequency')
+            samplingFrequency = logFile(1).SamplingFrequency;
+        end
+        if isfield(logFile, 'StartTime')
+            startTime = logFile(1).StartTime;
+        end
+
+        jsonContent = struct( ...
+                             'SamplingFrequency', samplingFrequency, ...
+                             'StartTime',  startTime, ...
+                             'Columns', []);
+    end
 
     % transfer content of extra fields to json content
     namesExtraColumns = returnNamesExtraColumns(logFile);
@@ -39,6 +62,10 @@ function createDataDictionary(cfg, logFile)
 
             headerName = returnHeaderName(namesExtraColumns{iExtraColumn}, nbCol, iCol);
 
+            if isfield(logFile, 'isStim') && ~isempty(logFile.isStim) && logFile.isStim
+                jsonContent.Columns{end + 1} = headerName;
+            end
+
             jsonContent.(headerName) = ...
                 logFile(1).extraColumns.(namesExtraColumns{iExtraColumn}).bids;
 
@@ -46,6 +73,4 @@ function createDataDictionary(cfg, logFile)
 
     end
 
-    bids.util.jsonencode(fileName, jsonContent, opts);
-
 end
diff --git a/src/createDatasetDescription.m b/src/createDatasetDescription.m
index 38e44fa2..2d16c694 100644
--- a/src/createDatasetDescription.m
+++ b/src/createDatasetDescription.m
@@ -1,10 +1,19 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function createDatasetDescription(cfg)
-    % createDatasetDescription(cfg)
     %
-    % creates the datasetDescription.json file that goes in the root of a BIDS
-    % dataset
+    % It creates ``dataset_description.json`` and writes in every entry contained in
+    % ``cfg.bids.datasetDescription``. The file should go in the root of a BIDS dataset.
+    %
+    % USAGE::
+    %
+    %   createDatasetDescription(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    %
+    % :output: - :``dataset_description.json``: (jsonfile)
+    %
 
     opts.Indent = '    ';
 
diff --git a/src/createFilename.m b/src/createFilename.m
index 4f6addb7..e8f41c63 100644
--- a/src/createFilename.m
+++ b/src/createFilename.m
@@ -1,20 +1,39 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function cfg = createFilename(cfg)
-    % cfg = createFilename(cfg)
     %
-    % create the BIDS compliant directories and fileNames for the behavioral output
-    % for this subject / session / run using the information from cfg and expParameters.
+    % It creates the BIDS compliant directories and fileNames for the behavioral output
+    % for this subject / session / run using the information from cfg.
+    %
+    % The folder tree will always include a session folder.
+    %
     % Will also create the right fileName for the eyetracking data file.
+    % For the moment the date of acquisition is appended to the fileName.
+    %
+    % USAGE::
+    %
+    %   [cfg] = createFilename(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    %
+    % :returns:
+    %
+    %           :cfg: (structure) Configuration update with the name of info about the
+    %                 participants.
     %
-    % For the moment the date of acquisition is appended to the fileName
+    % The behavior of this function depends on:
     %
-    % can work for behavioral experiment if cfg.device is set to 'PC'
-    % can work for fMRI experiment if cfg.device is set to 'scanner'
-    % can work for simple eyetracking data if cfg.eyeTracker.do is set to 1
+    %   - ``cfg.testingDevice``:
     %
+    %       + set to ``pc`` (dummy try) or ``beh`` can work for behavioral experiment.
+    %       + set on ``mri`` for fMRI experiment.
+    %       + set on ``eeg`` or ``ieeg`` can work for electro encephalography or intracranial eeg
+    %       + set on ``meg`` can work for magneto encephalography
     %
-    % See test_createFilename in the test folder for more details on how to use it.
+    %   - ``cfg.eyeTracker.do`` set to ``true``, can work for simple eyetracking data.
+    %
+    % See ``test_createFilename`` in the ``tests`` folder for more details on how to use it.
 
     cfg = checkCFG(cfg);
 
@@ -33,7 +52,20 @@
 
     cfg = setFilenames(cfg);
 
-    talkToMe(cfg);
+    talkToMe(cfg, sprintf('\nData will be saved in this directory:\n\t%s\n', ...
+                          fullfile(cfg.dir.outputSubject, cfg.fileName.modality)));
+
+    talkToMe(cfg, sprintf('\nData will be saved in this file:\n\t%s\n', cfg.fileName.events));
+
+    if cfg.eyeTracker.do
+
+        talkToMe(cfg, sprintf('\nEyetracking data will be saved in this directory:\n\t%s\n', ...
+                              fullfile(cfg.dir.outputSubject, 'eyetracker')));
+
+        talkToMe(cfg, sprintf('\nEyetracking data will be saved in this file:\n\t%s\n', ...
+                              cfg.fileName.eyetracker));
+
+    end
 
     cfg = orderfields(cfg);
     cfg.fileName = orderfields(cfg.fileName);
@@ -200,27 +232,3 @@
     end
 
 end
-
-function talkToMe(cfg)
-
-    if cfg.verbose > 0
-
-        fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
-                fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
-
-        fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
-                cfg.fileName.events);
-
-        if cfg.eyeTracker.do
-
-            fprintf(1, '\nEyetracking data will be saved in this directory:\n\t%s\n', ...
-                    fullfile(cfg.dir.outputSubject, 'eyetracker'));
-
-            fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
-                    cfg.fileName.eyetracker);
-
-        end
-
-    end
-
-end
diff --git a/src/createJson.m b/src/createJson.m
index fdc42a35..bf28117f 100644
--- a/src/createJson.m
+++ b/src/createJson.m
@@ -1,29 +1,38 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function createJson(varargin)
-    % createBoldJson(cfg, varargin)
     %
     % Creates the side car JSON file for a run.
-    % This will only contain the minimum BIDS requirement and will likey be less
-    % complete than the info you could from a proper conversion.
     %
-    % USAGE
+    % For JSON sidecars for bold files, this will only contain the minimum BIDS
+    % requirement and will likey be less complete than the info you could from
+    % a proper BIDS conversion.
     %
-    % createJson(cfg, modality)
+    % USAGE::
     %
-    %   modality is string ('beh', 'func', 'eeg', 'ieeg', 'meg') to specify which
-    %   JSON to save
+    %   createJson(cfg [, modality] [, extraInfo])
+    %   createJson(cfg [, extraInfo])
     %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    % :param modality: can be any of the following ``'beh'``, ``'func'``, ``'eeg'``,
+    %                  ``'ieeg'``, ``'meg'``) to specify which JSON to save. If it is not
+    %                  provided it will read from ``cfg.fileName.modality``.
+    % :type modality: string
+    % :param extraInfo: contains information in the JSON file. Beware
+    %                   that the BIDS validator is pretty strict on what information can
+    %                   go in a JSON so this can be useful to store additional information
+    %                   in your source dataset but it might have to be cleaned up to create
+    %                   a valid BIDS dataset.
+    % :type extraInfo: structure
     %
-    % createJson(cfg, extraInfo)
+    % :output:
+    %          - :``*.json``: (jsonfile) The file name corresponds to the run + suffix depending
+    %                         on the arguments passed in.
     %
-    %   extraInfo is a strcuture to add axtra content can be added to the JSON file
-    %
-    %
-    % createJson(cfg, modality, extraInfo)
-    %
-    %   both are possible
+    % .. TODO:
     %
+    %    - use input parser for this one
     %
 
     [cfg, modality, extraInfo] = checkInput(varargin);
@@ -37,11 +46,7 @@ function createJson(varargin)
     end
 
     fileName = strrep(fileName, '.tsv', '.json');
-
-    fileName = fullfile( ...
-                        cfg.dir.outputSubject, ...
-                        modality, ...
-                        fileName);
+    fullFilename = getFullFilename(fileName, cfg);
 
     %% add content of extraInfo to the JSON content
 
@@ -52,7 +57,7 @@ function createJson(varargin)
 
     %% save
     opts.Indent = '    ';
-    bids.util.jsonencode(fileName, jsonContent, opts);
+    bids.util.jsonencode(fullFilename, jsonContent, opts);
 
 end
 
diff --git a/src/gui/askForGroupAndOrSession.m b/src/gui/askForGroupAndOrSession.m
new file mode 100644
index 00000000..3393836f
--- /dev/null
+++ b/src/gui/askForGroupAndOrSession.m
@@ -0,0 +1,35 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function cfg = askForGroupAndOrSession(cfg)
+    %
+    % It checks ``cfg`` if ``group`` and ``session`` are recquired in ``cfg.subject.askGrpSess`` by
+    % the user. If not specified, it will add these as ``true`` by default.
+    %
+    % USAGE::
+    %
+    %   [cfg] = askForGroupAndOrSession(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    %
+    % :returns:
+    %           :cfg: (structure) Configuration update with the instructions if to ask for ``group``
+    %                 and ``session``.
+
+    askGrpSess = [true true];
+
+    if isfield(cfg, 'subject') && ...
+            isfield(cfg.subject, 'askGrpSess') && ...
+            ~isempty(cfg.subject.askGrpSess)
+
+        askGrpSess = cfg.subject.askGrpSess;
+
+    end
+
+    if numel(askGrpSess) < 2
+        askGrpSess(2) = 1;
+    end
+
+    cfg.subject.askGrpSess = askGrpSess;
+
+end
diff --git a/src/subfun/askUserCli.m b/src/gui/askUserCli.m
similarity index 59%
rename from src/subfun/askUserCli.m
rename to src/gui/askUserCli.m
index 46491136..3615d9f5 100644
--- a/src/subfun/askUserCli.m
+++ b/src/gui/askUserCli.m
@@ -1,9 +1,21 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function responses = askUserCli(questions, responses)
-    % response = askUserCli(questions)
     %
-    % command line interface to ask questions to user
+    % It shows the questions to ask in the command window and checks, when it is necessary, if the
+    % given input by the user is an integer.
+    %
+    % USAGE::
+    %
+    %   [responses] = askUserCli(questions, responses)
+    %
+    % :param questions: It contains the questions list to ask and if the response given to one
+    %                   question must be checked to be a positive integer.
+    % :type questions: structure
+    % :param responses: It contains the responses set by default.
+    % :type responses: cell
+    %
+    % :returns: - :responses: (cell) Response updated with the user inputs.
     %
 
     for iQuestion = 1:size(questions.questionsToAsk, 1)
diff --git a/src/subfun/askUserGui.m b/src/gui/askUserGui.m
similarity index 68%
rename from src/subfun/askUserGui.m
rename to src/gui/askUserGui.m
index a141c637..61ca3423 100644
--- a/src/subfun/askUserGui.m
+++ b/src/gui/askUserGui.m
@@ -1,6 +1,23 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function responses = askUserGui(questions, responses)
+    %
+    % It shows the questions to ask in in a GUI interface and checks, when it is necessary, if the
+    % given input by the user is a positive integer. If not, it keeps showing the
+    % GUI interface.
+    %
+    % USAGE::
+    %
+    %   [responses] = askUserGui(questions, responses)
+    %
+    % :param questions: It contains the questions list to ask and if the response given to one
+    %                   question must be checked to be an integer number.
+    % :type questions: structure
+    % :param responses: It contains the responses set by default.
+    % :type responses: cell
+    %
+    % :returns: - :responses: (cell) Response updated with the user inputs.
+    %
 
     % boolean for which question should be asked
     isQuestionToAsk = ~cellfun('isempty', questions.questionsToAsk(:, 1));
diff --git a/src/subfun/createQuestionList.m b/src/gui/createQuestionList.m
similarity index 64%
rename from src/subfun/createQuestionList.m
rename to src/gui/createQuestionList.m
index fc2c43b0..c817fcea 100644
--- a/src/subfun/createQuestionList.m
+++ b/src/gui/createQuestionList.m
@@ -1,6 +1,21 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function questions = createQuestionList(cfg)
+    %
+    % It creates a list of default questions to ask the users regarding the subj ID, the run number,
+    % the group ID (if recquired by user) and session nb (if recquired by user).
+    %
+    % USAGE::
+    %
+    %   [questions] = createQuestionList(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    %
+    % :returns:
+    %           :questions: (structure) It contains the questions list to ask and if the response
+    %                       given to one question must be checked to be a positive integer.
+    %
 
     cfg = askForGroupAndOrSession(cfg);
 
@@ -17,6 +32,8 @@
     if cfg.subject.askGrpSess(1)
         questions.questionsToAsk{1, 1} = questions.group;
         questions.questionsToAsk{1, 2} = false;
+    else
+        questions.questionsToAsk{1, 2} = false;
     end
 
     % the subject number
@@ -27,6 +44,8 @@
     if  cfg.subject.askGrpSess(2)
         questions.questionsToAsk{3, 1} = questions.session;
         questions.questionsToAsk{3, 2} = true;
+    else
+        questions.questionsToAsk{3, 2} = false;
     end
 
     % the run number
diff --git a/src/gui/getIsQuestionToAsk.m b/src/gui/getIsQuestionToAsk.m
new file mode 100644
index 00000000..f495fb50
--- /dev/null
+++ b/src/gui/getIsQuestionToAsk.m
@@ -0,0 +1,30 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function isQuestionToAsk = getIsQuestionToAsk(questions, responses)
+    %
+    % While using the GUI interface to input the experiment information, it flags any question that
+    % will be presented in the GUI. If a response is not valid (e.g. is not an integer) it will keep
+    % flagging it as a 'question to ask' and represent the GUI.
+    %
+    % USAGE::
+    %
+    %   isQuestionToAsk = getIsQuestionToAsk(questions, responses)
+    %
+    % :param questions: It contains the questions list to ask and if the response given to one
+    %                   question must be checked to be an integer.
+    % :type questions: structure
+    % :param responses: It contains the responses set by default or as input by the user
+    % :type responses: cell
+    %
+    % :returns: - :argout1: (type) (dimension)
+    %           - :argout2: (type) (dimension)
+    %
+
+    isQuestionToAsk = cell2mat(questions.questionsToAsk(:, 2));
+    for j = 1:size(isQuestionToAsk, 1)
+        input2check = str2double(responses{j});
+        isQuestionToAsk(j, 2) = ~isPositiveInteger(input2check);
+    end
+    isQuestionToAsk = all(isQuestionToAsk, 2);
+
+end
diff --git a/src/subfun/setDefaultResponses.m b/src/gui/setDefaultResponses.m
similarity index 50%
rename from src/subfun/setDefaultResponses.m
rename to src/gui/setDefaultResponses.m
index d9814c45..3376b736 100644
--- a/src/subfun/setDefaultResponses.m
+++ b/src/gui/setDefaultResponses.m
@@ -1,6 +1,20 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function [cfg, responses] = setDefaultResponses(cfg)
+    %
+    % It sets default responses to for all the entries regarding subject group and for
+    % session and run number. The defaults are choosen depending on ``cfg.debug.do``.
+    %
+    % USAGE::
+    %
+    %   [cfg, responses] = setDefaultResponses(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    %
+    % :returns: - :responses: (cell) It contains the response set by default
+    %           - :cfg: (structure) Configuration update with ``cfg.debug.do`` set to false if not
+    %                   set by the user.
+    %
 
     if nargin < 1
         cfg = struct('debug', []);
diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m
index 1f791bab..52bd1f2a 100644
--- a/src/readAndFilterLogfile.m
+++ b/src/readAndFilterLogfile.m
@@ -1,25 +1,37 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, varargin)
-    % outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, varargin)
     %
-    % It will display in the command window the content of the `output.tsv' filtered by one element
-    % of a target column.
+    % It will display in the command window the content of the ``output.tsv``
+    % filtered by one element of a target column.
     %
-    % INPUT:
+    % USAGE::
     %
-    %  - columnName: string, the header of the column where the content of insterest is stored
-    %    (e.g., for 'trigger' will be 'trial type')
-    %  - filterBy: string, the content of the column you want to filter out. It can take just
-    %    part of the content name (e.g., you want to display the triggers and you have
-    %    'trigger_motion' and 'trigger_static', 'trigger' as input will do)
-    %  - saveOutputTsv: boolean to save the filtered ouput
-    %  - varargin: either cfg (to display the last run output) or the file path as string
+    %   outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, tsvFile)
     %
-    % OUTPUT:
+    %   outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, cfg)
+    %
+    % :param columnName: the header of the column where the content of interest is stored
+    %                    (for example for ``trigger`` will be ``trial type``)
+    % :type columnName: string
+    % :param filterBy: the content of the column you want to filter out. It can take just
+    %                  part of the content name (for example, if you want to display the triggers
+    %                  and you have ``trigger_motion`` and ``trigger_static``,
+    %                  ``trigger`` as input will do)
+    % :type filterBy: string
+    % :param saveOutputTsv: flag to save the filtered output in a tsv file
+    % :type saveOutputTsv: boolean
+    % :param tsvFile: TSV file to filter
+    % :type tsvFile: string
+    % :param cfg: Configuration. See ``checkCFG()``. If ``cfg`` is given as input the name
+    %             of the TSV file to read will be infered from there.
+    % :type cfg: structure
+    %
+    % :returns:
+    %
+    %           :outputFiltered: dataset with only the specified content, to see it
+    %                            in the command window use ``display(outputFiltered)``.
     %
-    %  - outputFiltered: dataset with only the specified content, to see it in the command window
-    %    use display(outputFiltered)
 
     % Create tag to add to output file in case you want to save it
     outputFilterTag = ['_filteredBy-' columnName '_' filterBy '.tsv'];
diff --git a/src/saveEventsFile.m b/src/saveEventsFile.m
index 42976359..dd940677 100644
--- a/src/saveEventsFile.m
+++ b/src/saveEventsFile.m
@@ -1,65 +1,83 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
-function [logFile] = saveEventsFile(action, cfg, logFile)
-    % [logFile] = saveEventsFile(action, cfg, logFile)
+function logFile = saveEventsFile(action, cfg, logFile)
     %
     % Function to save output files for events that will be BIDS compliant.
     %
-    % USAGE
+    % USAGE::
     %
-    % [logFile] = saveEventsFile('init', [cfg], logFile)
-    % [logFile] = saveEventsFile('open', [cfg], logFile)
-    % [logFile] = saveEventsFile('open_stim', [cfg], logFile)
-    % [logFile] = saveEventsFile('save', [cfg], logFile)
-    % [logFile] = saveEventsFile('close', cfg, logFile)
+    %   [logFile] = saveEventsFile(action, cfg, logFile)
     %
-    % INPUTS
+    % :param action: Defines the operation to do. The different possibilities are
+    %                ``'init'``, ``'init_stim'``, ``'open'``, ``'save'`` or ``'close'``.
+    %                For more information on each case see below.
+    % :type action: string
+    % :param cfg: Configuration variable. See ``checkCFG()``.
+    % :type cfg: structure
+    % :param logFile: (n x 1) The ``logFile`` variable that contains the n events
+    %                 you want to save must be a nx1 structure.
+    % :type logFile: structure
     %
-    % logFile:
-    %   When you want to save your data logFile contains the data you want to save.
-    % The logFile variable that contains the n events you want to % save must be a nx1 structure.
-    % Each field will be saved in a separate column.
+    % .. todo:
+    %    - more details about how to structure the logFile variable
     %
-    % example:
-    % logFile(1,1).onset = 2;
-    % logFile(1,1).trial_type = 'motion_up';
-    % logFile(1,1).duration = 1;
-    % logFile(1,1).speed = 2;
-    % logFile(1,1).is_fixation = true;
+    % See ``tests/test_saveEventsFile()`` for more details on how to use it.
     %
-    % logFile(2,1).onset = 3;
-    % logFile(2,1).trial_type = 'static';
-    % logFile(2,1).duration = 4;
-    % logFile(2,1).is_fixation = 3;
+    % Example::
     %
+    %   logFile(1,1).onset = 2;
+    %   logFile(1,1).trial_type = 'motion_up';
+    %   logFile(1,1).duration = 1;
     %
-    % action:
-    %  - 'open': will create the file ID and return it in logFile.fileID using the information in
-    % the expParameters structure. This file ID is then reused when calling that function
-    % to save data into this file.
-    % This creates the header with the obligatory 'onset', 'trial_type', 'duration' required
-    % by BIDS and other columns can be specified in varargin.
+    % Actions:
     %
-    % example : logFile = saveEventsFile('open', cfg, [], 'direction', 'speed', 'target');
+    %   Example::
+    %
+    %     logFile = saveEventsFile('init', cfg, logFile)
+    %     logFile = saveEventsFile('init_stim', cfg, logFile)
+    %     logFile = saveEventsFile('open', cfg, logFile)
+    %     logFile = saveEventsFile('save', cfg, logFile)
+    %
+    %   - ``'init'`` and ``'init_stim'`` are used for events and stimuli tsv files respectively.
+    %     This initializes the extra columns to be save.
+    %
+    %   - ``'open'`` will create the file ID and return it in ``logFile.fileID`` using
+    %     the information in the ``cfg`` structure.
+    %     This file ID is then reused when calling that function to save data into this file.
+    %     This creates the header with the obligatory ``'onset'``, ``'duration'`` required
+    %     by BIDS and other columns can be specified in varargin.
+    %
+    %     Example::
+    %
+    %       logFile = saveEventsFile('open', cfg, logFile);
+    %
+    %   - ``'save'`` will save the data contained in logfile by using the file ID
+    %     ``logFile.fileID``.
+    %     If saving a stimulus file then the only the fields of ``logFile.extraColumns``
+    %     will be saved.
+    %     For regular _events.tsv files, then ``logFile`` must then contain:
     %
-    %  - 'save': will save the data contained in logfile by using the file ID logFile.fileID;
-    % logfile must then contain:
     %     - logFile.onset
-    %     - logFile.trial_type
     %     - logFile.duration
-    % The name of any extra column whose content must be saved should be listed in varargin.
     %
-    %  - 'close': closes the file with file ID logFile.fileID. If expParameters.verbose is set
-    % to true then this will tell you where the file is located.
+    %     Otherwise it will be skipped.
+    %
+    %     Example::
+    %
+    %       logFile = saveEventsFile('save', cfg, logFile);
+    %
+    %   - ``'close'`` closes the file with file ID ``logFile.fileID``.
+    %     If ``cfg.verbose`` is superior to ``1`` then this will tell you
+    %     where the file is located.
+    %
+    %     Example::
+    %
+    %       logFile = saveEventsFile('close', cfg, logFile)
+    %
     %
-    % See test_saveEventsFile in the test folder for more details on how to use it.
-
-    if nargin < 1
-        error('Missing action input');
-    end
 
     if nargin < 2
-        cfg = struct();
+        errorSaveEventsFile('missingArgument');
     end
 
     if nargin < 3 || isempty(logFile)
@@ -69,39 +87,54 @@
     switch action
 
         case 'init'
+            % flag to indicate that this will be an _events file
+            logFile(1).isStim = false;
 
-            logFile = initializeExtraColumns(logFile);
-
-        case 'open'
-
-            logFile(1).filename = cfg.fileName.events;
-
-            logFile = initializeFile(cfg, logFile);
+            if isfield(cfg, 'fileName') && ...
+                                        isfield(cfg.fileName, 'events') && ...
+                                        ~isempty(cfg.fileName.events)
+                logFile(1).filename = cfg.fileName.events;
+            else
+                logFile(1).filename = '';
+            end
+            logFile = initializeFile(logFile);
 
-        case 'open_stim'
+        case 'init_stim'
+            % flag to indicate that this will be an _stim file
+            logFile(1).isStim = true;
 
-            logFile(1).filename = cfg.fileName.stim;
+            if isfield(cfg, 'fileName') && ...
+                                        isfield(cfg.fileName, 'stim') && ...
+                                        ~isempty(cfg.fileName.stim)
+                logFile(1).filename = cfg.fileName.stim;
+            else
+                logFile(1).filename = '';
+            end
+            logFile = initializeStimFile(logFile);
 
-            logFile = initializeFile(cfg, logFile);
+        case 'open'
+            logFile = openFile(cfg, logFile);
 
         case 'save'
-
             checklLogFile('checkID', logFile);
             checklLogFile('type&size', logFile);
 
             logFile = saveToLogFile(logFile, cfg);
 
         case 'close'
-
             checklLogFile('checkID', logFile);
 
             % close txt log file
             fclose(logFile(1).fileID);
 
-            talkToMe(cfg, logFile);
+            message = sprintf('\nData were saved in this file:\n\n%s\n\n', ...
+                              fullfile( ...
+                                       cfg.dir.outputSubject, ...
+                                       cfg.fileName.modality, ...
+                                       logFile.filename));
+            talkToMe(cfg, message);
 
         otherwise
-
             errorSaveEventsFile('unknownActionType');
 
     end
@@ -115,24 +148,20 @@
     switch action
 
         case 'init'
-
             logFile = struct('filename', [], 'extraColumns', cell(1));
             logFile(1).filename = '';
 
         case 'checkID'
-
             if ~isfield(logFile(1), 'fileID') || isempty(logFile(1).fileID)
                 errorSaveEventsFile('missingFileID');
             end
 
         case 'type&size'
-
             if ~isstruct(logFile) || size(logFile, 2) > 1
                 errorSaveEventsFile('wrongLogSize');
             end
 
         case 'fields'
-
             for iFields = {'onset', 'trial_type', 'duration'}
                 if ~isfield(logFile, iFields) || isempty(logFile(iEvent).(iFields{1}))
                     logFile(iEvent).(iFields{1}) = nan;
@@ -145,14 +174,42 @@
 
 end
 
-function logFile = initializeFile(cfg, logFile)
+function logFile = initializeFile(logFile)
+    % This function creates the bids field structure for json files for the
+    % three basic bids event columns, and for all requested extra columns.
+    %
+    % Note that subfields (e.g. unit, levels etc. can be changed by the user
+    % before calling openFile.
+
+    % initialize holy trinity (onset, trial_type, duration) columns
+    logFile(1).columns = struct( ...
+                                'onset', struct( ...
+                                                'Description', ...
+                                                'time elapsed since experiment start', ...
+                                                'Units', 's'), ...
+                                'trial_type', struct( ...
+                                                     'Description', 'types of trial', ...
+                                                     'Levels', ''), ...
+                                'duration', struct( ...
+                                                   'Description', ...
+                                                   'duration of the event or the block', ...
+                                                   'Units', 's') ...
+                               );
+
+    logFile = initializeExtraColumns(logFile);
+
+end
 
+function logFile = initializeStimFile(logFile)
     logFile = initializeExtraColumns(logFile);
+end
+
+function logFile = openFile(cfg, logFile)
 
     createDataDictionary(cfg, logFile);
 
     % Initialize txt logfiles and empty fields for the standard BIDS
-    %  event file
+    % event file
     logFile(1).fileID = fopen( ...
                               fullfile( ...
                                        cfg.dir.outputSubject, ...
@@ -160,34 +217,36 @@
                                        logFile.filename), ...
                               'w');
 
-    % print the basic BIDS columns
-    fprintf(logFile(1).fileID, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
-    fprintf(1, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
+    if ~logFile(1).isStim
+        % print the basic BIDS columns
+        fprintf(logFile(1).fileID, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
+        fprintf(1, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
+
+        printHeaderExtraColumns(logFile);
 
-    printHeaderExtraColumns(logFile);
+        % next line so we start printing at the right place
+        fprintf(logFile(1).fileID, '\n');
+        fprintf(1, '\n');
 
-    % next line so we start printing at the right place
-    fprintf(logFile(1).fileID, '\n');
-    fprintf(1, '\n');
+    elseif logFile(1).isStim
+        % don't print column headers for _stim.tsv
+
+    end
 
 end
 
 function printHeaderExtraColumns(logFile)
     % print any extra column specified by the user
 
-    [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile);
-
+    [namesExtraColumns] = returnNamesExtraColumns(logFile);
     for iExtraColumn = 1:numel(namesExtraColumns)
 
         nbCol = returnNbColumns(logFile, namesExtraColumns{iExtraColumn});
 
         for iCol = 1:nbCol
-
             headerName = returnHeaderName(namesExtraColumns{iExtraColumn}, nbCol, iCol);
-
             fprintf(logFile(1).fileID, '\t%s', headerName);
             fprintf(1, '\t%s', headerName);
-
         end
 
     end
@@ -196,12 +255,11 @@ function printHeaderExtraColumns(logFile)
 
 function logFile = checkExtracolumns(logFile, iEvent, cfg)
     % loops through the extra columns
-    % if the field we are looking for does not exist or is empty in the
-    % action logFile structure we will write a n/a
+    % if the field we are looking for does not exist or is empty in the action logFile structure
+    % we will write a n/a
     % otherwise we write its content
 
     namesExtraColumns = returnNamesExtraColumns(logFile);
-
     for iExtraColumn = 1:numel(namesExtraColumns)
 
         nbCol = returnNbColumns(logFile, namesExtraColumns{iExtraColumn});
@@ -213,143 +271,154 @@ function printHeaderExtraColumns(logFile)
 
         data = checkInput(data);
 
-        data = nanPadding(data, nbCol);
+        data = nanPadding(cfg, data, nbCol);
 
         logFile(iEvent).(namesExtraColumns{iExtraColumn}) = data;
 
-        if ~ischar(data) && any(isnan(data))
-            warning('saveEventsFile:missingData', ...
-                    'Missing some %s data for this event.', namesExtraColumns{iExtraColumn});
+        if ~ischar(data)
 
-            if cfg.verbose > 1
-                disp(logFile(iEvent));
-            end
+            warningMessage = [];
+            if any(isnan(data))
+                warningMessage = sprintf( ...
+                                         'Missing some %s data for this event.', ...
+                                         namesExtraColumns{iExtraColumn});
 
-        elseif ~ischar(data) && all(isnan(data))
-            warning('Missing %s data for this event.', namesExtraColumns{iExtraColumn});
+            elseif all(isnan(data))
+                warningMessage = sprintf( ...
+                                         'Missing %s data for this event.', ...
+                                         namesExtraColumns{iExtraColumn});
+
+            end
+            throwWarning(cfg, 'saveEventsFile:missingData', warningMessage);
 
             if cfg.verbose > 1
                 disp(logFile(iEvent));
             end
+
         end
 
     end
 
 end
 
-function data = checkInput(data)
-    % check the data to write
-    % default will be 'n/a' for chars and NaN for numeric data
-    % for numeric data that don't have the expected length, it will be padded with NaNs
+function logFile = saveToLogFile(logFile, cfg)
 
-    if islogical(data) && data
-        data = 'true';
-    elseif islogical(data) && ~data
-        data = 'false';
-    end
+    % appends to the logfile all the data stored in the structure
+    % first with the standard BIDS data and then any extra things
+    for iEvent = 1:size(logFile, 1)
 
-    if ischar(data) && isempty(data) || strcmp(data, ' ')
-        data = 'n/a';
-    elseif isempty(data)
-        % important to not set this to n/a as we still need to check if this
-        % numeric valur has the right length and needs to be nan padded
-        data = nan;
-    end
+        logFile = checklLogFile('fields', logFile, iEvent, cfg);
 
-end
+        % check if this event should be skipped
+        skipEvent = false;
+        warningMessageID = [];
+        warningMessage = [];
 
-function data = nanPadding(data, expectedLength)
+        % if this is _events file, we skip events with onset or duration
+        % that are empty, nan or char.
+        if ~logFile(1).isStim
 
-    if nargin < 2
-        expectedLength = [];
-    end
+            onset = logFile(iEvent).onset;
+            duration = logFile(iEvent).duration;
 
-    if ~isempty(expectedLength) && isnumeric(data) && max(size(data)) < expectedLength
-        padding = expectedLength - max(size(data));
-        data(end + 1:end + padding) = nan(1, padding);
-    elseif ~isempty(expectedLength) && isnumeric(data) && max(size(data)) > expectedLength
-        warning('saveEventsFile:arrayTooLong', ...
-                'A field for this event is longer than expected. Truncating the extra values.');
-        data = data(1:expectedLength);
-    end
+            if any(cell2mat(cellfun(@isnan, {onset duration}, 'UniformOutput', false))) || ...
+               any(cellfun(@ischar, {onset duration})) || ...
+               any(isempty({onset duration}))
 
-end
+                skipEvent = true;
 
-function logFile = saveToLogFile(logFile, cfg)
+                warningMessageID = 'saveEventsFile:emptyEvent';
+                warningMessage = sprintf(['Skipping saving this event. \n '...
+                                          'onset: %s \n duration: %s \n'], ...
+                                         onset, ...
+                                         duration);
+            end
 
-    % appends to the logfile all the data stored in the structure
-    % first with the standard BIDS data and then any extra things
-    for iEvent = 1:size(logFile, 1)
+            % if this is _stim file, we skip missing events (i.e. events where
+            % all extra columns have NO values)
+        elseif logFile(1).isStim
 
-        logFile = checklLogFile('fields', logFile, iEvent, cfg);
+            namesExtraColumns = returnNamesExtraColumns(logFile);
+            isValid = ones(1, numel(namesExtraColumns));
 
-        onset = logFile(iEvent).onset;
-        duration = logFile(iEvent).duration;
-        trial_type = logFile(iEvent).trial_type;
+            for iExtraColumn = 1:numel(namesExtraColumns)
+                data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
+                if isempty(data) || all(isnan(data)) || (ischar(data) && strcmp(data, 'n/a'))
+                    isValid(iExtraColumn) = 0;
+                end
+            end
 
-        % we skip events with onset or duration that are empty, nan or char
-        if any(cell2mat(cellfun(@isnan, {onset duration}, 'UniformOutput', false))) || ...
-                any(cellfun(@ischar, {onset duration})) || ...
-                any(isempty({onset duration}))
+            if all(~isValid)
+                skipEvent = true;
 
-            warning('saveEventsFile:emptyEvent', ...
-                    '\nSkipping saving this event.\n onset: %s \n duration: %s\n', ...
-                    onset, ...
-                    duration);
+                warningMessageID = 'saveEventsFile:emptyEvent';
+                warningMessage = sprintf(['Skipping saving this event. \n', ...
+                                          'No values defined. \n']);
 
-        else
+            elseif any(~isValid)
+                skipEvent = false;
 
-            printData(logFile(1).fileID, onset, cfg);
-            printData(logFile(1).fileID, duration, cfg);
-            printData(logFile(1).fileID, trial_type, cfg);
+                warningMessageID = 'saveEventsFile:missingData';
+                warningMessage = sprintf('Missing some %s data for this event. \n', ...
+                                         namesExtraColumns{find(isValid)});
+            end
+        end
 
-            printExtraColumns(logFile, iEvent, cfg);
+        % now save the event to log file (if not skipping)
+        throwWarning(cfg, warningMessageID, warningMessage);
 
-            fprintf(logFile(1).fileID, '\n');
-            fprintf(1, '\n');
+        printToFile(cfg, logFile, skipEvent, iEvent);
 
-        end
     end
 
 end
 
-function printExtraColumns(logFile, iEvent, cfg)
-    % loops through the extra columns and print them
+function printToFile(cfg, logFile, skipEvent, iEvent)
 
-    namesExtraColumns = returnNamesExtraColumns(logFile);
+    if ~skipEvent
 
-    for iExtraColumn = 1:numel(namesExtraColumns)
+        if ~logFile(1).isStim
+            printData(logFile(1).fileID, logFile(iEvent).onset, cfg);
+            printData(logFile(1).fileID, logFile(iEvent).duration, cfg);
+            printData(logFile(1).fileID, logFile(iEvent).trial_type, cfg);
+        end
 
-        data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
+        printExtraColumns(logFile, iEvent, cfg);
 
-        printData(logFile(1).fileID, data, cfg);
+        fprintf(logFile(1).fileID, '\n');
+        fprintf(1, '\n');
 
     end
+end
 
+function printExtraColumns(logFile, iEvent, cfg)
+    % loops through the extra columns and print them
+    namesExtraColumns = returnNamesExtraColumns(logFile);
+    for iExtraColumn = 1:numel(namesExtraColumns)
+        data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
+        printData(logFile(1).fileID, data, cfg);
+    end
 end
 
 function printData(output, data, cfg)
     % write char
     % for numeric data we replace any nan by n/a
     if ischar(data)
-        fprintf(output, '%s\t', data);
-        if cfg.verbose > 0
-            fprintf(1, '%s\t', data);
-        end
+        content = sprintf('%s\t', data);
+        fprintf(output, content);
+        talkToMe(cfg, content);
+
     else
         for i = 1:numel(data)
             if isnan(data(i))
-                fprintf(output, '%s\t', 'n/a');
-                if cfg.verbose > 0
-                    fprintf(1, '%s\t', 'n/a');
-                end
+                content = sprintf('%s\t', 'n/a');
             else
-                fprintf(output, '%f\t', data(i));
-                if cfg.verbose > 0
-                    fprintf(1, '%f\t', data(i));
-                end
+                content = sprintf('%f\t', data(i));
             end
+            fprintf(output, content);
+            talkToMe(cfg, content);
         end
+
     end
 end
 
@@ -359,15 +428,16 @@ function printData(output, data, cfg)
     logFile(2:end) = [];
 
     namesColumns = {'onset', 'duration', 'trial_type'};
+    if logFile(1).isStim
+        namesColumns = {};
+    end
     namesExtraColumns = returnNamesExtraColumns(logFile);
     namesColumns = cat(2, namesColumns, namesExtraColumns');
 
     for iColumn = 1:numel(namesColumns)
-
         if isfield(logFile, namesColumns{iColumn})
             logFile = rmfield(logFile, namesColumns{iColumn});
         end
-
     end
 
 end
@@ -375,6 +445,10 @@ function printData(output, data, cfg)
 function errorSaveEventsFile(identifier)
 
     switch identifier
+        case 'missingArgument'
+            errorStruct.message = ['Missing arguments. Please specify <action input> ', ...
+                                   'and <cfg file> as the first two arguments'];
+
         case 'unknownActionType'
             errorStruct.message = 'unknown action for saveEventsFile';
 
@@ -388,18 +462,5 @@ function errorSaveEventsFile(identifier)
 
     errorStruct.identifier = ['saveEventsFile:' identifier];
     error(errorStruct);
-end
-
-function talkToMe(cfg, logFile)
-
-    if cfg.verbose > 0
-
-        fprintf(1, '\nData were saved in this file:\n\n%s\n\n', ...
-                fullfile( ...
-                         cfg.dir.outputSubject, ...
-                         cfg.fileName.modality, ...
-                         logFile.filename));
-
-    end
 
 end
diff --git a/src/subfun/askForGroupAndOrSession.m b/src/subfun/askForGroupAndOrSession.m
deleted file mode 100644
index bac91022..00000000
--- a/src/subfun/askForGroupAndOrSession.m
+++ /dev/null
@@ -1,21 +0,0 @@
-% (C) Copyright 2020 CPP_BIDS developers
-
-function cfg = askForGroupAndOrSession(cfg)
-
-    askGrpSess = [true true];
-
-    if isfield(cfg, 'subject') && ...
-            isfield(cfg.subject, 'askGrpSess') && ...
-            ~isempty(cfg.subject.askGrpSess)
-
-        askGrpSess = cfg.subject.askGrpSess;
-
-    end
-
-    if numel(askGrpSess) < 2
-        askGrpSess(2) = 1;
-    end
-
-    cfg.subject.askGrpSess = askGrpSess;
-
-end
diff --git a/src/subfun/createValidName.m b/src/subfun/createValidName.m
deleted file mode 100644
index 57b905d4..00000000
--- a/src/subfun/createValidName.m
+++ /dev/null
@@ -1,19 +0,0 @@
-% (C) Copyright 2020 CPP_BIDS developers
-
-function [name, nameValid] = createValidName(name)
-    % [taskName, taskNameValid] = createTaskName(taskName)
-    %
-    % Name of the task (for resting state use the "rest" prefix). No two tasks
-    % should have the same name. Task label is derived from this field by
-    % removing all non alphanumeric ([a-zA-Z0-9]) characters.
-
-    % camel case: upper case for first letter for all words but the first one
-    spaceIdx = regexp(name, '[a-zA-Z0-9]*', 'start');
-    name(spaceIdx(2:end)) = upper(name(spaceIdx(2:end)));
-
-    % remove invalid characters
-    [unvalidCharacters] = regexp(name, '[^a-zA-Z0-9]');
-    nameValid = name;
-    nameValid(unvalidCharacters) = [];
-
-end
diff --git a/src/subfun/getIsQuestionToAsk.m b/src/subfun/getIsQuestionToAsk.m
deleted file mode 100644
index a8446235..00000000
--- a/src/subfun/getIsQuestionToAsk.m
+++ /dev/null
@@ -1,12 +0,0 @@
-% (C) Copyright 2020 CPP_BIDS developers
-
-function isQuestionToAsk = getIsQuestionToAsk(questions, responses)
-
-    isQuestionToAsk = cell2mat(questions.questionsToAsk(:, 2));
-    for j = 1:size(isQuestionToAsk, 1)
-        input2check = str2double(responses{j});
-        isQuestionToAsk(j, 2) = ~isPositiveInteger(input2check);
-    end
-    isQuestionToAsk = all(isQuestionToAsk, 2);
-
-end
diff --git a/src/subfun/returnHeaderName.m b/src/subfun/returnHeaderName.m
deleted file mode 100644
index fe59cbc3..00000000
--- a/src/subfun/returnHeaderName.m
+++ /dev/null
@@ -1,13 +0,0 @@
-% (C) Copyright 2020 CPP_BIDS developers
-
-function headerName = returnHeaderName(columnName, nbCol, iCol)
-    % headerName = returnHeaderName(columnName, nbCol, iCol)
-    %
-
-    if nbCol == 1
-        headerName = sprintf('%s', columnName);
-    else
-        headerName = sprintf('%s_%02.0f', columnName, iCol);
-    end
-
-end
diff --git a/src/subfun/returnNamesExtraColumns.m b/src/subfun/returnNamesExtraColumns.m
deleted file mode 100644
index 39b17629..00000000
--- a/src/subfun/returnNamesExtraColumns.m
+++ /dev/null
@@ -1,13 +0,0 @@
-% (C) Copyright 2020 CPP_BIDS developers
-
-function [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile)
-    % [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile)
-    %
-
-    namesExtraColumns = [];
-
-    if isfield(logFile, 'extraColumns') && ~isempty(logFile(1).extraColumns)
-        namesExtraColumns = fieldnames(logFile(1).extraColumns);
-    end
-
-end
diff --git a/src/subfun/returnNbColumns.m b/src/subfun/returnNbColumns.m
deleted file mode 100644
index 18234a7d..00000000
--- a/src/subfun/returnNbColumns.m
+++ /dev/null
@@ -1,14 +0,0 @@
-% (C) Copyright 2020 CPP_BIDS developers
-
-function nbCol = returnNbColumns(logFile, nameExtraColumn)
-    % nbCol = returnNbColumns(logFile, nameExtraColumn)
-    %
-
-    thisExtraColumn = logFile(1).extraColumns.(nameExtraColumn);
-
-    nbCol = 1;
-
-    if isfield(thisExtraColumn, 'length')
-        nbCol = thisExtraColumn.length;
-    end
-end
diff --git a/src/templates/miss_hit.cfg b/src/templates/miss_hit.cfg
new file mode 100644
index 00000000..d86aaeb0
--- /dev/null
+++ b/src/templates/miss_hit.cfg
@@ -0,0 +1,9 @@
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
+line_length: 100
+regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
+
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 15
+metric "parameters": limit 5
\ No newline at end of file
diff --git a/src/templates/templateFunction.m b/src/templates/templateFunction.m
new file mode 100644
index 00000000..3ac5e46b
--- /dev/null
+++ b/src/templates/templateFunction.m
@@ -0,0 +1,35 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function [argout1, argout2] = templateFunction(argin1, argin2, argin3)
+    %
+    % Short description of what the function does goes here.
+    %
+    % USAGE::
+    %
+    %   [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3])
+    %
+    % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet,
+    %                consectetur adipiscing elit. Ut congue nec est ac lacinia.
+    % :type argin1: type
+    % :param argin2: optional argument and its default value. And some of the
+    %               options can be shown in litteral like ``this`` or ``that``.
+    % :type argin2: string
+    % :param argin3: (dimension) optional argument
+    % :type argin3: integer
+    %
+    % :returns:
+    %           :argout1: (type) (dimension)
+    %           :argout2: (type) (dimension)
+    %
+    % :output:
+    %           :file created: description
+    %           :other file created: description
+    %
+    % .. todo:
+    %
+    %    - item 1
+    %    - item 2
+
+    % The code goes below
+
+end
diff --git a/src/templates/templateFunctionExample.m b/src/templates/templateFunctionExample.m
new file mode 100644
index 00000000..de35ef59
--- /dev/null
+++ b/src/templates/templateFunctionExample.m
@@ -0,0 +1,42 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function templateFunctionExample()
+    % This function illustrates a documentation test defined for MOdox.
+    % Other than that it does absolutely nothinghort description of what
+    % the function does goes here.
+    %
+    % Examples:
+    %   a=2;
+    %   disp(a)
+    %   % Expected output is prefixed by '%||' as in the following line:
+    %   %|| 2
+    %   %
+    %   % The test continues because no interruption through whitespace,
+    %   % as the previous line used a '%' comment character;
+    %   % thus the 'a' variable is still in the namespace and can be
+    %   % accessed.
+    %   b=3+a;
+    %   disp(a+[3 4])
+    %   %|| [5 6]
+    %
+    %   % A new test starts here because the previous line was white-space
+    %   % only. Thus the 'a' and 'b' variables are not present here anymore.
+    %   % The following expression raises an error because the 'b' variable
+    %   % is not defined (and does not carry over from the previous test).
+    %   % Because the expected output indicates an error as well,
+    %   % the test passes
+    %   disp(b)
+    %   %|| error('Some error')
+    %
+    %   % A set of expressions is ignored if there is no expected output
+    %   % (that is, no lines starting with '%||').
+    %   % Thus, the following expression is not part of any test,
+    %   % and therefore does not raise an error.
+    %   error('this is never executed)
+    %
+    %
+    % % tests end here because test indentation has ended
+
+    % The code goes below
+
+end
diff --git a/src/templates/test_templateTest.m b/src/templates/test_templateTest.m
new file mode 100644
index 00000000..73b91769
--- /dev/null
+++ b/src/templates/test_templateTest.m
@@ -0,0 +1,29 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function test_suite = test_templateTest %#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_templateTestBasic()
+
+    %% set up
+
+    % cfg.input_1 = ...
+
+    %% use function to test
+
+    % actualOupout = foo(cfg);
+
+    %% assert that output content / type / size is what you expect
+
+    % expectedOuput = X;
+
+    % assertEqual(actualOupout, expectedOuput)
+
+    %% clean up (delete temporary files that were created)
+
+end
diff --git a/src/userInputs.m b/src/userInputs.m
index 9264bf8b..f7eb2ce3 100644
--- a/src/userInputs.m
+++ b/src/userInputs.m
@@ -1,17 +1,28 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function cfg = userInputs(cfg)
-    % cfg = userInputs(cfg)
     %
     % Get subject, run and session number and make sure they are
     % positive integer values.
-    % Will do ii with a graphic interface if possible.
+    % Can do a graphic user interface if ``cfg.useGUI`` is set to ``true``
     %
-    % expParameters.subject.askGrpSess
-    % a 1 X 2 array of booleans (default is [true true] ):
-    %    - the first value set to false will skip asking for the participants
-    %    group
-    %    - the second value set to false will skip asking for the session
+    % USAGE::
+    %
+    %   cfg = userInputs([cfg])
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    %
+    % :returns:
+    %
+    %           :cfg: (structure) Configuration update with the name of info about the
+    %                 participants.
+    %
+    % Behavior of this functions depends on ``cfg.subject.askGrpSess``
+    % a 1 X 2 array of booleans (default is ``[true true]``):
+    %
+    % - the first value set to ``false`` will skip asking for the participants group
+    % - the second value set to ``false`` will skip asking for the session
 
     if nargin < 1
         cfg = struct('debug', []);
diff --git a/src/subfun/checkCppBidsDependencies.m b/src/utils/checkCppBidsDependencies.m
similarity index 65%
rename from src/subfun/checkCppBidsDependencies.m
rename to src/utils/checkCppBidsDependencies.m
index c0d794ff..4512ee43 100644
--- a/src/subfun/checkCppBidsDependencies.m
+++ b/src/utils/checkCppBidsDependencies.m
@@ -1,29 +1,38 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function checkCppBidsDependencies(cfg)
-    % checkCppBidsDependencies()
     %
+    % Adds dependencies to the Matlab / Octave path and make sure we got all of them.
+    %
+    % USAGE::
+    %
+    %   checkCppBidsDependencies(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
 
     GITHUB_WORKSPACE = getenv('GITHUB_WORKSPACE');
 
     if strcmp(GITHUB_WORKSPACE, '/github/workspace')
 
         pth = GITHUB_WORKSPACE;
-        addpath(fullfile(pth, 'lib', 'JSONio'));
-        addpath(fullfile(pth, 'lib', 'bids-matlab'));
+        addpath(genpath(fullfile(pth, 'lib')));
 
     elseif isempty(GITHUB_WORKSPACE)  % local
 
         pth = fullfile(fileparts(mfilename('fullpath')), '..', '..');
+        addpath(fullfile(pth, 'lib', 'utils'));
+
+        pth = fullfile(fileparts(mfilename('fullpath')), '..', '..');
+        pth = abspath(pth);
+
         checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
         checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
 
-        addpath(fullfile(pth, 'src', 'subfun'));
+        addpath(genpath(fullfile(pth, 'src')));
 
     end
 
-    addpath(fullfile(pth, 'lib', 'utils'));
-
     printCreditsCppBids(cfg);
 
 end
diff --git a/src/utils/checkInput.m b/src/utils/checkInput.m
new file mode 100644
index 00000000..53704bc7
--- /dev/null
+++ b/src/utils/checkInput.m
@@ -0,0 +1,28 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function data = checkInput(data)
+    %
+    % Check the data to write and convert to the proper format if needed.
+    %
+    % Default will be 'n/a' for chars and NaN for numeric data.
+    %
+    % USAGE::
+    %
+    %   data = checkInput(data)
+    %
+
+    if islogical(data) && data
+        data = 'true';
+    elseif islogical(data) && ~data
+        data = 'false';
+    end
+
+    if ischar(data) && isempty(data) || strcmp(data, ' ')
+        data = 'n/a';
+    elseif isempty(data)
+        % Important to not set this to n/a as we might still need to check if this
+        % numeric value has the right length and needs to be nan padded
+        data = nan;
+    end
+
+end
diff --git a/src/utils/createValidName.m b/src/utils/createValidName.m
new file mode 100644
index 00000000..27036a2f
--- /dev/null
+++ b/src/utils/createValidName.m
@@ -0,0 +1,42 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function [name, nameValid] = createValidName(name)
+    %
+    % Creates a BIDS valid name: for the task in file names.
+    %
+    % USAGE::
+    %
+    %   [taskName, taskNameValid] = createTaskName(taskName)
+    %
+    % :param taskName: Name given to the task. Can be any string including spaces
+    %                  and special characters.
+    % :type taskName: string
+    %
+    % :returns:
+    %           :name: (string) returns the input with an upper case for first letter
+    %                  for all words but the first one (``camelCase``).
+    %           :nameValid: (string) same as above but removes invalid characters (like spaces).
+    %
+    % Name of the task (for resting state use the "rest" prefix). No two tasks
+    % should have the same name. Task label is derived from this field by
+    % removing all non alphanumeric ([a-zA-Z0-9]) characters.
+    %
+    % Example:
+    % % taskName = 'foo bar';
+    % % [taskName, taskNameValid] = createValidName(taskName);
+    % % disp(taskName),
+    % % || 'foo Bar'
+    % % disp(taskNameValid)
+    % % || 'fooBar'
+    %
+
+    % camel case: upper case for first letter for all words but the first one
+    spaceIdx = regexp(name, '[a-zA-Z0-9]*', 'start');
+    name(spaceIdx(2:end)) = upper(name(spaceIdx(2:end)));
+
+    % remove invalid characters
+    [unvalidCharacters] = regexp(name, '[^a-zA-Z0-9]');
+    nameValid = name;
+    nameValid(unvalidCharacters) = [];
+
+end
diff --git a/src/utils/getFullFilename.m b/src/utils/getFullFilename.m
new file mode 100644
index 00000000..47ec96bd
--- /dev/null
+++ b/src/utils/getFullFilename.m
@@ -0,0 +1,22 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function fullFilename = getFullFilename(fileName, cfg)
+    %
+    % Returns the full path of a file (fo a given subject and modality in a run).
+    %
+    % USAGE::
+    %
+    %   fullFilename = getFullFilename(fileName, cfg)
+    %
+    % :param fileName:
+    % :type fileName: string
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    %
+
+    fullFilename = fullfile( ...
+                            cfg.dir.outputSubject, ...
+                            cfg.fileName.modality, ...
+                            fileName);
+
+end
diff --git a/src/subfun/initializeExtraColumns.m b/src/utils/initializeExtraColumns.m
similarity index 70%
rename from src/subfun/initializeExtraColumns.m
rename to src/utils/initializeExtraColumns.m
index ef1dad32..40cc86cd 100644
--- a/src/subfun/initializeExtraColumns.m
+++ b/src/utils/initializeExtraColumns.m
@@ -1,17 +1,31 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function logFile = initializeExtraColumns(logFile)
-    % logFile = initializeExtraColumns(logFile)
-    %    initialize the fields for the extra columns
-    %    USAGE
-    %       logfile.extraColumns{'Speed', 'Response key'}
-    %       logFile = initializeExtraColumns(logFile)
+    %
+    % Initialize the fields for the extra columns
+    %
+    % USAGE::
+    %
+    %   logFile = initializeExtraColumns(logFile)
+    %
+    % :param logFile: It contains what to save in the experiment outputs.
+    % :type logFile: structure
+    %
+    % :returns: :logFile: (structure) ``logfile`` updated with extra columns.
+    %
+    % Example::
+    %
+    %   logfile.extraColumns{'Speed', 'Response key'}
+    %   logFile = initializeExtraColumns(logFile)
+    %
+    %
 
     fieldsToSet.length = 1;
     fieldsToSet.bids.LongName = '';
     fieldsToSet.bids.Description = '';
     fieldsToSet.bids.Levels = '';
     fieldsToSet.bids.TermURL = '';
+    fieldsToSet.bids.Units = '';
 
     % convert the cell of column name into a structure
     if iscell(logFile(1).extraColumns)
diff --git a/src/subfun/isPositiveInteger.m b/src/utils/isPositiveInteger.m
similarity index 52%
rename from src/subfun/isPositiveInteger.m
rename to src/utils/isPositiveInteger.m
index e3598544..0058ca09 100644
--- a/src/subfun/isPositiveInteger.m
+++ b/src/utils/isPositiveInteger.m
@@ -1,9 +1,17 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function trueOrFalse = isPositiveInteger(input2check)
-    % trueOrFalse = isPositiveInteger(input2check)
     %
-    % works on column vector of values
+    % It checks whether the input is a positive integer and report it as ``true`` or ``false``
+    %
+    % USAGE::
+    %
+    %   trueOrFalse = isPositiveInteger(input2check)
+    %
+    % :param input2check: (1xn) The input to check (either a number or ``NaN``)
+    % :type input2check: vector
+    %
+    % :returns: :trueOrFalse: (boolean)
     %
 
     trueOrFalse = ~any([ ...
diff --git a/src/utils/nanPadding.m b/src/utils/nanPadding.m
new file mode 100644
index 00000000..2f8c05d9
--- /dev/null
+++ b/src/utils/nanPadding.m
@@ -0,0 +1,34 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function data = nanPadding(cfg, data, expectedLength)
+    %
+    % For numeric data that don't have the expected length, it will be padded
+    % with NaNs. If the vector is too long it will be truncated
+    %
+    % USAGE::
+    %
+    %  data = nanPadding(cfg, data, expectedLength)
+    %
+    %
+
+    if nargin < 2
+        expectedLength = [];
+    end
+
+    if ~isempty(expectedLength) && isnumeric(data)
+
+        if max(size(data)) < expectedLength
+            padding = expectedLength - max(size(data));
+            data(end + 1:end + padding) = nan(1, padding);
+
+        elseif max(size(data)) > expectedLength
+            warningMessage = ['A field for this event is longer than expected.', ...
+                              'Truncating extra values.'];
+            throwWarning(cfg, 'nanPadding:arrayTooLong', warningMessage);
+
+            data = data(1:expectedLength);
+
+        end
+    end
+
+end
diff --git a/src/subfun/printCreditsCppBids.m b/src/utils/printCreditsCppBids.m
similarity index 79%
rename from src/subfun/printCreditsCppBids.m
rename to src/utils/printCreditsCppBids.m
index 03947463..ed8bced2 100644
--- a/src/subfun/printCreditsCppBids.m
+++ b/src/utils/printCreditsCppBids.m
@@ -1,6 +1,17 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function printCreditsCppBids(cfg)
+    %
+    % It will print the credits of this repo. Depending on the level of verbosity set in
+    % ``cfg.verbose`` (default is 2 if not set), it will print the graphic and general information.
+    %
+    % USAGE::
+    %
+    %   printCreditsCppBids(cfg)
+    %
+    % :param cfg: Configuration. See ``checkCFG()``.
+    % :type cfg: structure
+    %
 
     try
         version = fileread(fullfile(fileparts(mfilename('fullpath')), ...
@@ -17,9 +28,10 @@ function printCreditsCppBids(cfg)
     if verbose > 1
 
         contributors = { ...
-                        'Rémi Gau', ...
+                        'Remi Gau', ...
                         'Marco Barilari', ...
-                        'Ceren Battal'};
+                        'Ceren Battal', ...
+                        'Tomas Lenc'};
 
         DOI_URL = 'https://doi.org/10.5281/zenodo.4007674';
 
diff --git a/src/subfun/removeAllDateSuffix.m b/src/utils/removeAllDateSuffix.m
similarity index 71%
rename from src/subfun/removeAllDateSuffix.m
rename to src/utils/removeAllDateSuffix.m
index d7ddba32..946cf4a6 100644
--- a/src/subfun/removeAllDateSuffix.m
+++ b/src/utils/removeAllDateSuffix.m
@@ -1,8 +1,26 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function removeAllDateSuffix(rawDir, subjName, sesName)
-    % removeAllDateSuffix(rawDir, subjName, sesName)
     %
+    % Function removes the date suffix in the _events and _stim (.tsv and .json)
+    % files in given raw, session and subject folder. And zips the _stim files.
+    % Function will look for files with suffix of ``_date-*``
+    %
+    % USAGE::
+    %
+    %   removeAllDateSuffix(rawDir, subjName, sesName)
+    %
+    % :param rawDir: BIDS raw folder directory.
+    % :type rawDir: string
+    %
+    % :param subjName: Some of the options can be ``sub-001`` or ``sub-pilot001``.
+    % :type subjName: string
+    %
+    % :param sesName: Some of the options can be ``ses-001`` or ``ses-003``.
+    % :type sesName: string
+
+    % :output: - files are renamed by removing '_date-*' suffix
+    %         and _stim files are zipped
 
     labels = {'func', 'bold', 'eeg', 'ieeg', 'meg', 'beh'};
 
diff --git a/src/subfun/removeDateSuffix.m b/src/utils/removeDateSuffix.m
similarity index 61%
rename from src/subfun/removeDateSuffix.m
rename to src/utils/removeDateSuffix.m
index ab04cbb2..1ed96087 100644
--- a/src/subfun/removeDateSuffix.m
+++ b/src/utils/removeDateSuffix.m
@@ -1,9 +1,22 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function removeDateSuffix(filenames, subjectPath)
-    % removeDateSuffix(filenames, subjectPath)
     %
+    % Function removes the date suffix in a given filename(s)
+    % Function will look for regular expression in filenames with ``_date-``
+
+    %
+    % USAGE::
+    %
+    %   removeDateSuffix(filenames, subjectPath)
+    %
+    % :param filenames: File names with _date- suffix
+    % :type filenames: string
+    %
+    % :param subjectPath: Location/path of the files
+    % :type subjectPath: string
     %
+    % :output: - files are renamed by removing '_date-*' suffix
 
     if isempty(filenames)
         filenames = {};
diff --git a/src/utils/returnHeaderName.m b/src/utils/returnHeaderName.m
new file mode 100644
index 00000000..682fc40c
--- /dev/null
+++ b/src/utils/returnHeaderName.m
@@ -0,0 +1,27 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function headerName = returnHeaderName(columnName, nbCol, iCol)
+    %
+    % It returns one by one the column name to be used as a header in a recently opened event file
+    %
+    % USAGE::
+    %
+    %   headerName = returnHeaderName(columnName, nbCol, iCol)
+    %
+    % :param columnName: The column name to print
+    % :type columnName: string
+    % :param nbCol: It is the number of columns associated to one entry of the extra column list
+    % :type nbCol: integer
+    % :param iCol: Index of the columns associated to one entry of the extra column list
+    % :type iCol: integer
+    %
+    % :returns: - :headerName: (string) return the extra column name to be used as header
+    %
+
+    if nbCol == 1
+        headerName = sprintf('%s', columnName);
+    else
+        headerName = sprintf('%s_%02.0f', columnName, iCol);
+    end
+
+end
diff --git a/src/utils/returnNamesExtraColumns.m b/src/utils/returnNamesExtraColumns.m
new file mode 100644
index 00000000..5e14d669
--- /dev/null
+++ b/src/utils/returnNamesExtraColumns.m
@@ -0,0 +1,24 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function [namesExtraColumns] = returnNamesExtraColumns(logFile)
+    %
+    % It returns the extra columns name(s), in ``cfg.extraColumns``,  as header to add to the
+    % ``event`` file
+    %
+    % USAGE::
+    %
+    %   [namesExtraColumns] = returnNamesExtraColumns(logFile)
+    %
+    % :param logFile: It contains all the information to be saved in the event/stim file
+    % :type logFile: structure
+    %
+    % :returns: - :namesExtraColumns: (cell) (nx1)
+    %
+
+    namesExtraColumns = [];
+
+    if isfield(logFile, 'extraColumns') && ~isempty(logFile(1).extraColumns)
+        namesExtraColumns = fieldnames(logFile(1).extraColumns);
+    end
+
+end
diff --git a/src/utils/returnNbColumns.m b/src/utils/returnNbColumns.m
new file mode 100644
index 00000000..48c9da85
--- /dev/null
+++ b/src/utils/returnNbColumns.m
@@ -0,0 +1,28 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function nbCol = returnNbColumns(logFile, nameExtraColumn)
+    %
+    % It returns the number of columns associated to one entry of the extra column list.
+    %
+    % USAGE::
+    %
+    %   [nbCol] = returnNbColumns(logFile, nameExtraColumn)
+    %
+    % :param logFile: It contains every information related to the experiment output(s)
+    % :type logFile: structure
+    % :param nameExtraColumn: An entry of ``logFile.extraColumns``
+    % :type nameExtraColumn: string
+    %
+    % :returns:
+    %           - :nbCol: (integer) The number of columns associated to one entry of the extra
+    %                     column list.
+    %
+
+    thisExtraColumn = logFile(1).extraColumns.(nameExtraColumn);
+
+    nbCol = 1;
+
+    if isfield(thisExtraColumn, 'length')
+        nbCol = thisExtraColumn.length;
+    end
+end
diff --git a/src/subfun/setDefaultFields.m b/src/utils/setDefaultFields.m
similarity index 68%
rename from src/subfun/setDefaultFields.m
rename to src/utils/setDefaultFields.m
index 6cfad781..abcfdc16 100644
--- a/src/subfun/setDefaultFields.m
+++ b/src/utils/setDefaultFields.m
@@ -1,9 +1,20 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function structure = setDefaultFields(structure, fieldsToSet)
-    % structure = setDefaultFields(structure, fieldsToSet)
     %
-    % recursively loop through the fields of a structure and sets a value if they don't exist
+    % Recursively loop through the fields of a structure and sets a default value if
+    % they don't exist.
+    %
+    % USAGE::
+    %
+    %   structure = setDefaultFields(structure, fieldsToSet)
+    %
+    % :param structure: Structure to check.
+    % :type structure: structure
+    % :param fieldsToSet: Structure containing the defaults for the missing fields.
+    % :type fieldsToSet: structure
+    %
+    % :returns: :structure: (structure)
     %
 
     fieldsToSet = orderfields(fieldsToSet);
diff --git a/src/utils/talkToMe.m b/src/utils/talkToMe.m
new file mode 100644
index 00000000..3c97b463
--- /dev/null
+++ b/src/utils/talkToMe.m
@@ -0,0 +1,7 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function talkToMe(cfg, message)
+    if cfg.verbose > 0
+        fprintf(1, message);
+    end
+end
diff --git a/src/utils/throwWarning.m b/src/utils/throwWarning.m
new file mode 100644
index 00000000..25bbf38e
--- /dev/null
+++ b/src/utils/throwWarning.m
@@ -0,0 +1,11 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function throwWarning(cfg, identifier, warningMessage)
+    if cfg.verbose > 0 && ...
+            nargin == 3 && ...
+            ~isempty(identifier) && ...
+            ~isempty(warningMessage)
+
+        warning(identifier, warningMessage);
+    end
+end
diff --git a/src/subfun/transferInfoToBids.m b/src/utils/transferInfoToBids.m
similarity index 56%
rename from src/subfun/transferInfoToBids.m
rename to src/utils/transferInfoToBids.m
index f21950fd..cdb464d5 100644
--- a/src/subfun/transferInfoToBids.m
+++ b/src/utils/transferInfoToBids.m
@@ -1,10 +1,27 @@
 % (C) Copyright 2020 CPP_BIDS developers
 
 function fieldsToSet = transferInfoToBids(fieldsToSet, cfg)
-    % fieldsToSet = transferInfoToBids(fieldsToSet, cfg)
     %
-    % transfer any info that might have been provided by the user to the
-    % relevant field for its reuse for BIDS filenames or JSON later
+    % Transfers any info that might have been provided
+    % by the user in ``cfg`` to the relevant field of ``fieldsToSet``
+    % for its reuse later for BIDS filenames or JSON.
+    %
+    % USAGE::
+    %
+    %   fieldsToSet = transferInfoToBids(fieldsToSet, cfg)
+    %
+    % :param fieldsToSet: List of the fields to set. See ``checkCFG()``.
+    % :type fieldsToSet: structure
+    % :param cfg: The configuration variable where the user has predefined some fields.
+    %             See ``checkCFG()``.
+    % :type cfg: structure
+    %
+    % :returns: :fieldsToSet: Updated list of the fields to set.
+    %
+    % This can be used for example to make sure that the repetition time set
+    % manually in ``cfg.mri.repetitionTime`` or in ``cfg.task.name``
+    % will be passed to the correct field in right fields of ``cfg.bids``.
+    %
 
     if isfield(cfg, 'task') && isfield(cfg.task, 'name')
         [taskName, taskNameValid] = createValidName(cfg.task.name);
diff --git a/src/subfun/utilsForTests/setUp.m b/src/utils/utilsForTests/setUp.m
similarity index 73%
rename from src/subfun/utilsForTests/setUp.m
rename to src/utils/utilsForTests/setUp.m
index fa29d4f4..ec282c03 100644
--- a/src/subfun/utilsForTests/setUp.m
+++ b/src/utils/utilsForTests/setUp.m
@@ -2,7 +2,7 @@
 
 function [cfg, logFile] = setUp()
 
-    cfg.verbose = true;
+    cfg.verbose = 2;
 
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
@@ -13,6 +13,10 @@
 
     cfg = createFilename(cfg);
 
+    logFile.extraColumns = {'Speed', 'LHL24', 'is_Fixation'};
+
+    logFile = saveEventsFile('init', cfg, logFile);
+
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 12;
     logFile.extraColumns.is_Fixation.length = 1;
diff --git a/tests/miss_hit.cfg b/tests/miss_hit.cfg
index f59bdb02..d86aaeb0 100644
--- a/tests/miss_hit.cfg
+++ b/tests/miss_hit.cfg
@@ -1,7 +1,6 @@
 # style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
-suppress_rule: "copyright_notice"
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 4
diff --git a/manualTests/testData/eventsDataDictionary.json b/tests/testData/eventsDataDictionary.json
similarity index 75%
rename from manualTests/testData/eventsDataDictionary.json
rename to tests/testData/eventsDataDictionary.json
index 45570965..877f159d 100644
--- a/manualTests/testData/eventsDataDictionary.json
+++ b/tests/testData/eventsDataDictionary.json
@@ -1,7 +1,7 @@
 {
     "onset": {
         "Description": "time elapsed since experiment start",
-        "Unit": "s"
+        "Units": "s"
     },
     "trial_type": {
         "Description": "types of trial",
@@ -9,30 +9,34 @@
     },
     "duration": {
         "Description": "duration of the event or the block",
-        "Unit": "s"
+        "Units": "s"
     },
     "Speed": {
         "LongName": "",
         "Description": "",
         "Levels": "",
-        "TermURL": ""
+        "TermURL": "",
+        "Units": ""
     },
     "LHL24_01": {
         "LongName": "",
         "Description": "",
         "Levels": "",
-        "TermURL": ""
+        "TermURL": "",
+        "Units": ""
     },
     "LHL24_02": {
         "LongName": "",
         "Description": "",
         "Levels": "",
-        "TermURL": ""
+        "TermURL": "",
+        "Units": ""
     },
     "LHL24_03": {
         "LongName": "",
         "Description": "",
         "Levels": "",
-        "TermURL": ""
+        "TermURL": "",
+        "Units": ""
     }
 }
\ No newline at end of file
diff --git a/manualTests/testData/extra_bold.json b/tests/testData/extra_bold.json
similarity index 100%
rename from manualTests/testData/extra_bold.json
rename to tests/testData/extra_bold.json
diff --git a/tests/testData/stimDataDictionary.json b/tests/testData/stimDataDictionary.json
new file mode 100644
index 00000000..39490c72
--- /dev/null
+++ b/tests/testData/stimDataDictionary.json
@@ -0,0 +1,46 @@
+{
+    "SamplingFrequency": 100,
+    "StartTime": 0,
+    "Columns": [
+        "Speed",
+        "LHL24_01",
+        "LHL24_02",
+        "LHL24_03",
+        "is_Fixation"
+    ],
+    "Speed": {
+        "Description": "",
+        "Levels": "",
+        "LongName": "",
+        "TermURL": "",
+        "Units": ""
+    },
+    "LHL24_01": {
+        "Description": "",
+        "Levels": "",
+        "LongName": "",
+        "TermURL": "",
+        "Units": ""
+    },
+    "LHL24_02": {
+        "Description": "",
+        "Levels": "",
+        "LongName": "",
+        "TermURL": "",
+        "Units": ""
+    },
+    "LHL24_03": {
+        "Description": "",
+        "Levels": "",
+        "LongName": "",
+        "TermURL": "",
+        "Units": ""
+    },
+    "is_Fixation": {
+        "Description": "",
+        "Levels": "",
+        "LongName": "",
+        "TermURL": "",
+        "Units": ""
+    }
+}
\ No newline at end of file
diff --git a/tests/test_askForGroupAndOrSession.m b/tests/test_askForGroupAndOrSession.m
index cfa91a0a..e01e1918 100644
--- a/tests/test_askForGroupAndOrSession.m
+++ b/tests/test_askForGroupAndOrSession.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_askForGroupAndOrSession %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/tests/test_checkCFG.m b/tests/test_checkCFG.m
index dc2edc90..b2c9d787 100644
--- a/tests/test_checkCFG.m
+++ b/tests/test_checkCFG.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_checkCFG %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -103,7 +105,6 @@ function test_checkCfgBasic()
     expectedCfgStructure.suffix.reconstruction = [];
     expectedCfgStructure.suffix.echo = [];
     expectedCfgStructure.suffix.acquisition = [];
-    expectedCfgStructure.suffix.repetitionTime = [];
     expectedCfgStructure.suffix.recording = [];
 
     expectedCfgStructure.bids.beh.TaskName = '';
diff --git a/tests/test_checkInput.m b/tests/test_checkInput.m
new file mode 100644
index 00000000..518b60d4
--- /dev/null
+++ b/tests/test_checkInput.m
@@ -0,0 +1,34 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function test_suite = test_checkInput %#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_checkInputBasic()
+
+    data = checkInput(1);
+    assertEqual(data, 1);
+
+    data = checkInput('test');
+    assertEqual(data, 'test');
+
+    data = checkInput('');
+    assertEqual(data, 'n/a');
+
+    data = checkInput(' ');
+    assertEqual(data, 'n/a');
+
+    data = checkInput([]);
+    assertEqual(data, nan);
+
+    data = checkInput(true());
+    assertEqual(data, 'true');
+
+    data = checkInput(false());
+    assertEqual(data, 'false');
+
+end
diff --git a/tests/test_createDataDictionary.m b/tests/test_createDataDictionary.m
new file mode 100644
index 00000000..fab77536
--- /dev/null
+++ b/tests/test_createDataDictionary.m
@@ -0,0 +1,151 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function test_suite = test_createDataDictionary %#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_createDataDictionaryBasic()
+
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
+
+    %% set up
+
+    cfg.verbose = false;
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'mri';
+
+    cfg = createFilename(cfg);
+
+    logFile.extraColumns = {'Speed', 'LHL24'};
+
+    logFile = saveEventsFile('init', cfg, logFile);
+
+    logFile.extraColumns.Speed.length = 1;
+    logFile.extraColumns.LHL24.length = 3;
+
+    logFile = saveEventsFile('open', cfg, logFile);
+
+    %% check that the file has the right path and name
+
+    % data to test against
+    funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
+
+    jsonFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
+                    cfg.fileName.date '.json'];
+
+    % test
+    assertTrue(exist(fullfile(funcDir, jsonFilename), 'file') == 2);
+
+    %% check content
+
+    return
+
+    % TODO fix error in CI
+    % failure: /github/workspace/lib/JSONio/jsonread.mex: failed to load:
+    %    liboctinterp.so.4: cannot open shared object file: No such file or directory
+    % jsondecode:27 (/github/workspace/lib/bids-matlab/+bids/+util/jsondecode.m)
+    % test_createDataDictionary>test_createDataDictionaryBasic:48
+    %   (/github/workspace/tests/test_createDataDictionary.m)
+    %
+    %     failure: fileread: cannot open file
+    %     fileread:37 (/octave/share/octave/5.2.0/m/io/fileread.m)
+    %     jsondecode:27 (/github/workspace/lib/bids-matlab/+bids/+util/jsondecode.m)
+    %     test_createDataDictionary>test_createDataDictionaryBasic:62
+
+    actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
+
+    % data to test against
+    expectedStruct = bids.util.jsondecode( ...
+                                          fullfile( ...
+                                                   pwd, ...
+                                                   'testData', ...
+                                                   'eventsDataDictionary.json'));
+
+    % test
+    assertTrue(isequal(expectedStruct, actualStruct));
+
+end
+
+function test_createDataDictionaryStim()
+
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
+
+    %% set up
+
+    cfg.verbose = false;
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'mri';
+
+    cfg = createFilename(cfg);
+
+    stimLogFile.extraColumns = {'Speed', 'LHL24', 'is_Fixation'};
+
+    stimLogFile = saveEventsFile('init_stim', cfg, stimLogFile);
+
+    stimLogFile.extraColumns.Speed.length = 1;
+    stimLogFile.extraColumns.LHL24.length = 3;
+    stimLogFile.extraColumns.is_Fixation.length = 1;
+
+    stimLogFile.SamplingFrequency = 100;
+    stimLogFile.StartTime = 0;
+
+    stimLogFile = saveEventsFile('open', cfg, stimLogFile);
+
+    %% check that the file has the right path and name
+
+    % data to test against
+    funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
+
+    jsonFilename = ['sub-001_ses-001_task-testtask_run-001_stim_date-' ...
+                    cfg.fileName.date '.json'];
+
+    % test
+    assertTrue(exist(fullfile(funcDir, jsonFilename), 'file') == 2);
+
+    %% check content
+
+    return
+
+    % TODO fix error in CI
+    % failure: /github/workspace/lib/JSONio/jsonread.mex: failed to load:
+    %    liboctinterp.so.4: cannot open shared object file: No such file or directory
+    % jsondecode:27 (/github/workspace/lib/bids-matlab/+bids/+util/jsondecode.m)
+    % test_createDataDictionary>test_createDataDictionaryBasic:48
+    %   (/github/workspace/tests/test_createDataDictionary.m)
+    %
+    %     failure: fileread: cannot open file
+    %     fileread:37 (/octave/share/octave/5.2.0/m/io/fileread.m)
+    %     jsondecode:27 (/github/workspace/lib/bids-matlab/+bids/+util/jsondecode.m)
+    %     test_createDataDictionary>test_createDataDictionaryStim:128
+
+    actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
+
+    % data to test against
+    expectedStruct = bids.util.jsondecode( ...
+                                          fullfile( ...
+                                                   pwd, ...
+                                                   'testData', ...
+                                                   'stimDataDictionary.json'));
+
+    % test
+    assertTrue(isequal(expectedStruct, actualStruct));
+
+end
diff --git a/manualTests/test_createDatasetDescription.m b/tests/test_createDatasetDescription.m
similarity index 89%
rename from manualTests/test_createDatasetDescription.m
rename to tests/test_createDatasetDescription.m
index c4664eb0..3d96c9e5 100644
--- a/manualTests/test_createDatasetDescription.m
+++ b/tests/test_createDatasetDescription.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_createDatasetDescription %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -8,7 +10,7 @@
 
 function test_createDatasetDescriptionBasic()
 
-    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
 
     %% set up
 
diff --git a/tests/test_createFilename.m b/tests/test_createFilename.m
index 36f5b546..89721fee 100644
--- a/tests/test_createFilename.m
+++ b/tests/test_createFilename.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_createFilename %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/tests/test_createJson.m b/tests/test_createJson.m
index e4f67b2b..90b01027 100644
--- a/tests/test_createJson.m
+++ b/tests/test_createJson.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_createJson %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -126,6 +128,60 @@ function test_createJsonIeeg()
 
 end
 
+function test_createJsonExtra()
+
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
+
+    %% set up
+
+    cfg.verbose = false;
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'mri';
+
+    cfg = createFilename(cfg);
+
+    logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
+
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+
+    createJson(cfg, extraInfo);
+
+    %% check content
+    fileName = strrep(cfg.fileName.events, '_events', '_bold');
+    fileName = strrep(fileName, '.tsv', '.json');
+
+    % TODO fix error in CI
+    %     failure: /github/workspace/lib/JSONio/jsonread.mex: failed to load: liboctinterp.so.4:
+    %     cannot open shared object file: No such file or directory
+    %     jsondecode:27 (/github/workspace/lib/bids-matlab/+bids/+util/jsondecode.m)
+    %     test_createJson>test_createJsonExtra:158 (/github/workspace/tests/test_createJson.m)
+    %
+    %     failure: fileread: cannot open file
+    %     fileread:37 (/octave/share/octave/5.2.0/m/io/fileread.m)
+    %     jsondecode:27 (/github/workspace/lib/bids-matlab/+bids/+util/jsondecode.m)
+    %     test_createJson>test_createJsonExtra:180 (/github/workspace/tests/test_createJson.m)
+
+    actualStruct = bids.util.jsondecode(fullfile( ...
+                                                 cfg.dir.outputSubject, ...
+                                                 cfg.fileName.modality, ...
+                                                 fileName));
+
+    return
+
+    expectedStruct = bids.util.jsondecode(fullfile(pwd, 'testData', 'extra_bold.json'));
+
+    % test
+    assertEqual(expectedStruct, actualStruct);
+
+end
+
 function cfg = setUp()
 
     cfg.verbose = false;
diff --git a/tests/test_createQuestionList.m b/tests/test_createQuestionList.m
index 88a9e08c..f8be1412 100644
--- a/tests/test_createQuestionList.m
+++ b/tests/test_createQuestionList.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_createQuestionList %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -19,6 +21,24 @@ function test_createQuestionListBasic()
                     'Enter the session number (i.e day ; 1-999): ', true
                     'Enter the run number (1-999): ', true};
 
-    assertEqual(expectedCell(3, 1), questions.questionsToAsk(3, 1));
+    assertEqual(expectedCell, questions.questionsToAsk);
+
+end
+
+function test_createQuestionListRestricted()
+
+    %% set up
+    cfg = struct();
+    cfg.subject.askGrpSess = [false false];
+
+    questions = createQuestionList(cfg);
+
+    expectedCell = { ...
+                    [], false
+                    'Enter subject number (1-999): ', true
+                    [], false
+                    'Enter the run number (1-999): ', true};
+
+    assertEqual(expectedCell, questions.questionsToAsk);
 
 end
diff --git a/tests/test_createValidName.m b/tests/test_createValidName.m
index d191c0ac..44890365 100644
--- a/tests/test_createValidName.m
+++ b/tests/test_createValidName.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_createValidName %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -10,7 +12,7 @@ function test_createTaskNameRemoveInvalidCharacters()
 
     %% set up
 
-    taskName = '&|@#-_(§!{})[]ù%£+/=:;.?,\<> visual task';
+    taskName = '&|@#-_(!{})[]%+/=:;.?,\<> visual task';
 
     [~, taskNameValid] = createValidName(taskName);
 
diff --git a/tests/test_getIsQuestionToAsk.m b/tests/test_getIsQuestionToAsk.m
index a53b0892..94aaf0d1 100644
--- a/tests/test_getIsQuestionToAsk.m
+++ b/tests/test_getIsQuestionToAsk.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_getIsQuestionToAsk %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/tests/test_isPositiveInteger.m b/tests/test_isPositiveInteger.m
index 9945ff5e..beaf0902 100644
--- a/tests/test_isPositiveInteger.m
+++ b/tests/test_isPositiveInteger.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_isPositiveInteger %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/tests/test_nanPadding.m b/tests/test_nanPadding.m
new file mode 100644
index 00000000..4758dade
--- /dev/null
+++ b/tests/test_nanPadding.m
@@ -0,0 +1,48 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
+function test_suite = test_nanPadding %#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_nanPaddingBasic()
+
+    cfg.verbose = 1;
+
+    %%
+    data = 'test';
+    expectedLength = 2;
+
+    data = nanPadding(cfg, data, expectedLength);
+
+    assertEqual(data, 'test');
+
+    %%
+    data = [1 0];
+    expectedLength = 2;
+
+    data = nanPadding(cfg, data, expectedLength);
+
+    assertEqual(data, [1 0]);
+
+    %%
+    data = [1 0];
+    expectedLength = 3;
+
+    data = nanPadding(cfg, data, expectedLength);
+
+    assertEqual(data, [1 0 NaN]);
+
+    %%
+    %%
+    data = [1 0 1];
+    expectedLength = 2;
+
+    data = nanPadding(cfg, data, expectedLength);
+
+    assertEqual(data, [1 0]);
+
+end
diff --git a/tests/test_readAndFilterLogfile.m b/tests/test_readAndFilterLogfile.m
index 81406ed5..cba936a7 100644
--- a/tests/test_readAndFilterLogfile.m
+++ b/tests/test_readAndFilterLogfile.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_readAndFilterLogfile %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -9,8 +11,8 @@
 function test_readAndFilterLogfileBasic()
 
     %% set up
-    cfg.dir.output = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
     [cfg, logFile] = setUp();
+    cfg.dir.output = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
diff --git a/tests/test_removeDateSuffix.m b/tests/test_removeDateSuffix.m
index edb360af..e13f95a2 100644
--- a/tests/test_removeDateSuffix.m
+++ b/tests/test_removeDateSuffix.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_removeDateSuffix %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/tests/test_saveEventsFileInit.m b/tests/test_saveEventsFileInit.m
index d56fe165..059e2f85 100644
--- a/tests/test_saveEventsFileInit.m
+++ b/tests/test_saveEventsFileInit.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_saveEventsFileInit %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -15,14 +17,24 @@ function test_saveEventsFileInitBasic()
     % make sure the dependencies are there
     checkCFG(cfg);
 
-    [logFile] = saveEventsFile('init');
+    [logFile] = saveEventsFile('init', cfg);
 
     %% data to test against
     expectedStrcut(1).filename = '';
     expectedStrcut(1).extraColumns = [];
+    expectedStrcut(1).isStim = false;
+
+    expectedStrcut(1).columns.onset.Description = 'time elapsed since experiment start';
+    expectedStrcut(1).columns.onset.Units = 's';
+
+    expectedStrcut(1).columns.trial_type.Description = 'types of trial';
+    expectedStrcut(1).columns.trial_type.Levels = '';
+
+    expectedStrcut(1).columns.duration.Description = 'duration of the event or the block';
+    expectedStrcut(1).columns.duration.Units = 's';
 
     %% test
-    assertEqual(expectedStrcut, logFile);
+    assertTrue(isequal(expectedStrcut, logFile));
 
 end
 
@@ -39,11 +51,13 @@ function test_saveEventsFileInitExtraColumns()
     [logFile] = saveEventsFile('init', cfg, logFile);
 
     %% data to test against
+    expectedStrcut = saveEventsFile('init', cfg);
     expectedStrcut(1).extraColumns.Speed.length = 1;
     expectedStrcut(1).extraColumns.Speed.bids.LongName = '';
     expectedStrcut(1).extraColumns.Speed.bids.Description = '';
     expectedStrcut(1).extraColumns.Speed.bids.Levels = '';
     expectedStrcut(1).extraColumns.Speed.bids.TermURL = '';
+    expectedStrcut(1).extraColumns.Speed.bids.Units = '';
 
     %% test
     assertEqual(expectedStrcut, logFile);
@@ -64,16 +78,19 @@ function test_saveEventsFileInitExtraColumnsArray()
     [logFile] = saveEventsFile('init', cfg, logFile);
 
     %% data to test against
+    expectedStrcut = saveEventsFile('init', cfg);
     expectedStrcut(1).extraColumns.Speed.length = 1;
     expectedStrcut(1).extraColumns.Speed.bids.LongName = '';
     expectedStrcut(1).extraColumns.Speed.bids.Description = '';
     expectedStrcut(1).extraColumns.Speed.bids.Levels = '';
     expectedStrcut(1).extraColumns.Speed.bids.TermURL = '';
+    expectedStrcut(1).extraColumns.Speed.bids.Units = '';
     expectedStrcut(1).extraColumns.LHL24.length = 3;
     expectedStrcut(1).extraColumns.LHL24.bids.LongName = '';
     expectedStrcut(1).extraColumns.LHL24.bids.Description = '';
     expectedStrcut(1).extraColumns.LHL24.bids.Levels = '';
     expectedStrcut(1).extraColumns.LHL24.bids.TermURL = '';
+    expectedStrcut(1).extraColumns.LHL24.bids.Units = '';
 
     %% test
     assertEqual(expectedStrcut, logFile);
diff --git a/tests/test_saveEventsFileOpen.m b/tests/test_saveEventsFileOpen.m
index d09d9aaa..91f0738c 100644
--- a/tests/test_saveEventsFileOpen.m
+++ b/tests/test_saveEventsFileOpen.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_saveEventsFileOpen %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -25,8 +27,10 @@ function test_saveEventsFileOpenBasic()
 
     cfg = createFilename(cfg);
 
+    logFile = saveEventsFile('init', cfg);
+
     % create the events file and header
-    logFile = saveEventsFile('open', cfg);
+    logFile = saveEventsFile('open', cfg, logFile);
 
     % close the file
     saveEventsFile('close', cfg, logFile);
@@ -70,29 +74,22 @@ function test_saveEventsFileOpenStimfile()
 
     cfg = createFilename(cfg);
 
+    logFile = saveEventsFile('init_stim', cfg);
+
     % create the events file and header
-    logFile = saveEventsFile('open_stim', cfg);
+    logFile = saveEventsFile('open', cfg, logFile);
 
     % close the file
     saveEventsFile('close', cfg, logFile);
 
     %% data to test against
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
-    eventFilename = ['sub-001_ses-001_task-testtask_run-001_stim_date-' ...
-                     cfg.fileName.date '.tsv'];
+    stimFilename = ['sub-001_ses-001_task-testtask_run-001_stim_date-' ...
+                    cfg.fileName.date '.tsv'];
 
     % check that the file has the right path and name
-    assert(exist(fullfile(funcDir, eventFilename), 'file') == 2);
-    assert(exist(fullfile(funcDir, strrep(eventFilename, '.tsv', '.json')), 'file') == 2);
-
-    FID = fopen(fullfile(funcDir, eventFilename), 'r');
-    C = textscan(FID, repmat('%s', 1, 3), 'Delimiter', '\t', 'EndOfLine', '\n');
-
-    %% test
-    % check the extra columns of the header
-    assertEqual(C{1}{1}, 'onset');
-    assertEqual(C{2}{1}, 'duration');
-    assertEqual(C{3}{1}, 'trial_type');
+    assert(exist(fullfile(funcDir, stimFilename), 'file') == 2);
+    assert(exist(fullfile(funcDir, strrep(stimFilename, '.tsv', '.json')), 'file') == 2);
 
 end
 
@@ -120,6 +117,8 @@ function test_saveEventsFileOpenExtraColumns()
     % they will be added to the tsv files in the order the user input them
     logFile.extraColumns = {'Speed', 'is_Fixation'};
 
+    logFile = saveEventsFile('init', cfg, logFile);
+
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
 
diff --git a/tests/test_saveEventsFileOpenMultiColumn.m b/tests/test_saveEventsFileOpenMultiColumn.m
index 05e63f41..8b88cbc1 100644
--- a/tests/test_saveEventsFileOpenMultiColumn.m
+++ b/tests/test_saveEventsFileOpenMultiColumn.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_saveEventsFileOpenMultiColumn %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -25,11 +27,15 @@ function test_saveEventsFileOpenMultiColumnCheckHeader()
 
     cfg = createFilename(cfg);
 
-    % define the extra columns: here we specify how many columns we want for
-    % each variable
+    % define the extra columns names
+    logFile.extraColumns = {'Speed', 'LHL24', 'is_Fixation'};
+
+    % initalize logfile
+    logFile = saveEventsFile('init', cfg, logFile);
+
+    % extra columns: here we specify how many columns we want for each variable
     logFile.extraColumns.Speed.length = 1; % will set 1 columns with name Speed
     logFile.extraColumns.LHL24.length = 12; % will set 12 columns with names LHL24-01, LHL24-02, ...
-    logFile.extraColumns.is_Fixation = []; % will set 1 columns with name is_Fixation
 
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
diff --git a/tests/test_saveEventsFileSave.m b/tests/test_saveEventsFileSave.m
index 971000bd..7d65805d 100644
--- a/tests/test_saveEventsFileSave.m
+++ b/tests/test_saveEventsFileSave.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_saveEventsFileSave %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
@@ -44,13 +46,70 @@ function test_saveEventsFileSaveBasic()
 
 end
 
+function test_saveEventsFileSaveStim()
+
+    %% set up
+
+    cfg.verbose = 2;
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
+
+    cfg.testingDevice = 'mri';
+
+    cfg = createFilename(cfg);
+
+    logFile.extraColumns = {'Speed', 'LHL24', 'is_Fixation'};
+
+    logFile = saveEventsFile('init_stim', cfg, logFile);
+
+    logFile.extraColumns.Speed.length = 1;
+    logFile.extraColumns.LHL24.length = 3;
+    logFile.extraColumns.is_Fixation.length = 1;
+
+    % create the events file and header
+    logFile = saveEventsFile('open', cfg, logFile);
+
+    % ROW 2: normal events : all info is there
+    logFile(1, 1).onset = 2;
+    logFile(end, 1).trial_type = 'motion_up';
+    logFile(end, 1).duration = 3;
+    logFile(end, 1).Speed = 2;
+    logFile(end, 1).LHL24 = 1:3;
+    logFile(end, 1).is_Fixation = true;
+
+    logFile = saveEventsFile('save', cfg, logFile);
+
+    % close the file
+    saveEventsFile('close', cfg, logFile);
+
+    % check the extra columns of the header and some of the content
+    nbExtraCol = ...
+        logFile(1).extraColumns.Speed.length + ...
+        logFile(1).extraColumns.LHL24.length + ...
+        logFile(1).extraColumns.is_Fixation.length;
+
+    funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
+
+    FID = fopen(fullfile(funcDir, logFile.filename), 'r');
+    content = textscan(FID, repmat('%s', 1, nbExtraCol), 'Delimiter', '\t', 'EndOfLine', '\n');
+
+    % event 1/ ROW 2: check that values are entered correctly
+    assertEqual(content{1}{1}, sprintf('%f', 2));
+    assertEqual(content{4}{1}, sprintf('%f', 3));
+    assertEqual(content{5}{1}, 'true');
+
+end
+
 function test_saveEventsFileSaveSkipEmptyEvents()
 
     %% set up
 
     [cfg, logFile] = setUp();
 
-    cfg.verbose = false;
+    cfg.verbose = 1;
 
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
@@ -142,7 +201,7 @@ function test_saveEventsFileSaveArraySize()
 
     [cfg, logFile] = setUp();
 
-    cfg.verbose = false;
+    cfg.verbose = 1;
 
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
@@ -163,7 +222,7 @@ function test_saveEventsFileSaveArraySize()
     logFile(end, 1).duration = 3;
     logFile(end, 1).LHL24 = rand(1, 15);
 
-    assertWarning(@()saveEventsFile('save', cfg, logFile), 'saveEventsFile:arrayTooLong');
+    assertWarning(@()saveEventsFile('save', cfg, logFile), 'nanPadding:arrayTooLong');
 
     saveEventsFile('save', cfg, logFile);
 
diff --git a/tests/test_setDefaultFields.m b/tests/test_setDefaultFields.m
index 39ca05d4..1a9d5dd4 100644
--- a/tests/test_setDefaultFields.m
+++ b/tests/test_setDefaultFields.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_setDefaultFields %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/tests/test_setDefaultResponses.m b/tests/test_setDefaultResponses.m
index 90500326..a8df533c 100644
--- a/tests/test_setDefaultResponses.m
+++ b/tests/test_setDefaultResponses.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_setDefaultResponses %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/tests/test_transferInfoToBids.m b/tests/test_transferInfoToBids.m
index 555331a0..d68b544c 100644
--- a/tests/test_transferInfoToBids.m
+++ b/tests/test_transferInfoToBids.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_transferInfoToBids %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/tests/test_utils.m b/tests/test_utils.m
index d7f4d771..2dc86ee2 100644
--- a/tests/test_utils.m
+++ b/tests/test_utils.m
@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP_BIDS developers
+
 function test_suite = test_utils %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
diff --git a/version.txt b/version.txt
index 60453e69..6eaf8943 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-v1.0.0
\ No newline at end of file
+v2.0.0
\ No newline at end of file