diff --git a/.github/workflows/check_markdown.yml b/.github/workflows/check_markdown.yml
deleted file mode 100644
index 1b997e3d..00000000
--- a/.github/workflows/check_markdown.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-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 *.md --frail
-        npx remark ./docs/ --frail
-        npx remark ./demos/ --frail
-        npx remark ./tests/ --frail
diff --git a/.github/workflows/miss_hit.yml b/.github/workflows/miss_hit_quality.yml
similarity index 86%
rename from .github/workflows/miss_hit.yml
rename to .github/workflows/miss_hit_quality.yml
index 5c5e561d..9ff86d1f 100644
--- a/.github/workflows/miss_hit.yml
+++ b/.github/workflows/miss_hit_quality.yml
@@ -1,4 +1,4 @@
-name: miss_hit
+name: miss_hit_quality
 
 on:
   push:
@@ -29,10 +29,6 @@ jobs:
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
 
-    - name: MISS_HIT Code style
-      run: |
-        mh_style --process-slx
-
     - name: MISS_HIT Metrics
       run: |
         mh_metric --ci
diff --git a/.github/workflows/miss_hit_style.yml b/.github/workflows/miss_hit_style.yml
new file mode 100644
index 00000000..17e5bdca
--- /dev/null
+++ b/.github/workflows/miss_hit_style.yml
@@ -0,0 +1,35 @@
+name: miss_hit_style
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install -r requirements.txt
+
+    - name: MISS_HIT Code style
+      run: |
+        mh_style
+
diff --git a/.github/workflows/run_system_tests.yml b/.github/workflows/run_system_tests.yml
index 8f0f845e..2761d9c6 100644
--- a/.github/workflows/run_system_tests.yml
+++ b/.github/workflows/run_system_tests.yml
@@ -56,20 +56,9 @@ jobs:
          make -C spm12/src PLATFORM=octave install
          octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
         
-    - name: Update octave path
-      run: |
-        octave $OCTFLAGS --eval "initCppSpm; savepath();"       
-
-    - name: Prepare data
-      run: |
-        inputs_folder='demos/MoAE/inputs/'
-        mkdir $inputs_folder
-        curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $inputs_folder'MoAEpilot.zip'
-        unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
-        mv $inputs_folder/MoAEpilot $inputs_folder/raw
-
+    
     - name: Run system tests
       run: |
-        cd demos/MoAE
-        octave $OCTFLAGS --eval "MoAEpilot_run"                  
+        cd manualTests/
+        octave $OCTFLAGS --eval "systemTestMoAE"                  
 
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 3ad370d8..b9f64864 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -78,7 +78,7 @@ jobs:
 
     - name: Run tests
       run: |
-        octave $OCTFLAGS --eval "runTests"
+        octave $OCTFLAGS --eval "run_tests"
         cat test_report.log | grep 0
         bash <(curl -s https://codecov.io/bash)         
 
diff --git a/.gitignore b/.gitignore
index d520b176..f0a8a647 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,6 +29,7 @@ docs/build/*
 
 # ignore virtual env
 cpp_spm/*
+env/*
 
 # visual studio code stuff
 .vscode
diff --git a/.remarkrc b/.remarkrc
deleted file mode 100644
index 201ce70e..00000000
--- a/.remarkrc
+++ /dev/null
@@ -1,11 +0,0 @@
-{
-  "plugins": [
-    "preset-lint-consistent",
-    "preset-lint-markdown-style-guide",
-    "preset-lint-recommended",
-    ["lint-no-duplicate-headings", false],
-    ["lint-list-item-indent", "tab-size"],
-    ["lint-maximum-line-length", true],
-    ["lint-maximum-heading-length", false]
-  ]
-}
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
deleted file mode 100644
index 88b79e16..00000000
--- a/CONTRIBUTING.md
+++ /dev/null
@@ -1,346 +0,0 @@
-# Contributing
-
-## Unit testing
-
-All tests are in the test folder. There is also an empty dummy BIDS dataset that
-is partly created using the bash script `createDummyDataSet.sh`.
-
-## Changelog
-
-<!-- github_changelog_generator -u cpp-lln-lab -p CPP_BIDS_SPM_pipeline --token 93b4c584bf22883a3c4f8b9031b70e381deef272 -->
-
-<!-- 
-
-
-# Contributing to the BIDS Specification
-
-**Welcome to the BIDS Specification repository!**
-
-*We're so excited you're here and want to contribute.*
-
-We hope that these guidelines are designed to make it as easy as possible to get involved. If you have any questions that aren't discussed below, please let us know by [opening an issue](#understanding-issues).
-
-## Joining the community
-
-BIDS - the [Brain Imaging Data Structure](https://bids.neuroimaging.io/) - is a growing community of neuroimaging enthusiasts, and we want to make our resources accessible to and engaging for as many researchers as possible.
-
-How do you know that you're a member of the BIDS community? You're here! You know that BIDS exists! You're officially a member of the community. It's THAT easy! Welcome!
-
-Most of our discussions take place here in [GitHub issues](#understanding-issues).
-We also have a [bids-discussion](https://groups.google.com/forum/#!forum/bids-discussion) Google Group, although this is largely now an archive of previous conversations.
-
-Moving forward, we encourage all members to contribute here on [GitHub](https://github.com/bids-standard/bids-specification) or on the [NeuroStars](https://neurostars.org/tags/bids) Discourse Forum, under the `bids` tag.
-
-To keep on top of new posts, please see this guide for setting your [topic notifications](https://meta.discourse.org/t/discourse-new-user-guide/96331#heading--topic-notifications).
-
-As a reminder, we expect that all contributions adhere to our [Code of Conduct](CODE_OF_CONDUCT.md).
-
-## Contributing through GitHub
-
-[Git](https://git-scm.com/) is a really useful tool for version control. [GitHub](https://github.com/) sits on top of git and supports collaborative and distributed working.
-
-We know that it can be daunting to start using git and GitHub if you haven't worked with them in the past, but the BIDS Specification maintainers are here to help you figure out any of the jargon or confusing instructions you encounter!
-
-In order to contribute via GitHub you'll need to set up a free account and sign in. Here are some [instructions](https://help.github.com/articles/signing-up-for-a-new-github-account/) to help you get going. Remember that you can ask us any questions you need to along the way.
-
-## Understanding issues
-
-Every project on GitHub uses [issues](https://github.com/bids-standard/bids-specification/issues) slightly differently.
-
-The following outlines how BIDS developers think about communicating through issues.
-
-**Issues** are individual pieces of work that need to be completed or decisions that need to be made to move the project forwards.
-A general guideline: if you find yourself tempted to write a great big issue that
-is difficult to describe as one unit of work, please consider splitting it into two or more issues.
-
-Issues are assigned [labels](#issue-labels) which explain how they relate to the overall project's goals and immediate next steps.
-
-### Issue labels
-
-The current list of labels are [here](https://github.com/bids-standard/bids-specification/labels) and include:
-
-* [![Help wanted](https://img.shields.io/badge/-help%20wanted-159818.svg)](https://github.com/bids-standard/bids-specification/labels/community) *These issues contain a task that a member of the team has determined we need additional help with.*
-
-    If you feel that you can contribute to one of these issues, we especially encourage you to do so!
-
-* [![Opinions wanted](https://img.shields.io/badge/-opinions%20wanted-84b6eb.svg)](https://github.com/bids-standard/bids-specification/labels/opinions%20wanted) *These issues hold discussions where we're especially eager for feedback.*
-
-    Ongoing discussions benefit from broad feedback.
-    This label is used to highlight issues where decisions are being considered, so please join the conversation!
-
-* [![Community](https://img.shields.io/badge/-community-%23ddcc5f.svg)](https://github.com/bids-standard/bids-specification/labels/community) *These issues are related to building and supporting the BIDS community.*
-
-    In addition to the specification itself, we are dedicated to creating a healthy community.
-    These issues highlight pieces of work or discussions around how we can support our members and make it easier to contribute.
-
-## Commenting on a pull request
-
-Our primary method of adding to or enhancing BIDS occurs in the form of [pull requests](https://help.github.com/articles/about-pull-requests/).
-BIDS Extension Proposals ([BEPs](https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/)) are submitted as pull requests, and commenting on pull requests is an important way of participating in the BIDS community.
-
-This section outlines how to comment on a pull request.
-
-### Navigating to open pull requests
-
-The list of pull requests can be found by clicking on the "Pull requests" tab in the [BIDS-Specification repository](https://github.com/bids-standard/bids-specification).
-
-![BIDS-mainpage](commenting_images/BIDS_GitHub_mainpage.png "BIDS_GitHub_mainpage")
-
-### Selecting an open pull request
-
-In this example we will be navigating to our [BIDS common derivatives pull request](https://github.com/bids-standard/bids-specification/pull/265).
-
-![BIDS-pr-list](commenting_images/BIDS_pr_list.png "BIDS_pr_list")
-
-### Pull request description
-
-Upon opening the pull request we see a detailed description of what this pull request is seeking to address.
-Descriptions are important for reviewers and the community to gain context into what the pull request is achieving.
-
-![BIDS-pr](commenting_images/BIDS_pr.png "BIDS_pr")
-
-### Generally commenting on a pull request
-
-At the bottom of the pull request page, a comment box is provided for general comments and questions.
-
-![BIDS-comment](commenting_images/BIDS_comment.png "BIDS-comment")
-
-### Specific comments on a pull request
-
-The proposed changes to the text of the specification can be seen in the "Files changed" tab.
-Proposed additions are displayed on a green background with a `+` before each added line.
-Proposed deletions are displayed on a red background with a `-` before each removed line.
-To comment on a specific line, hover over it, and click the blue plus sign (pictured below).
-Multiple lines can be selected by clicking and dragging the plus sign.
-
-![BIDS-specific-comment](commenting_images/BIDS_file_comment.png "BIDS-specific-comment")
-
-#### Suggesting text
-
-Comments on lines can contain "suggestions", which allow you to propose specific wording for consideration.
-To make a suggestion, click the plus/minus (±) icon in the comment box (pictured below).
-
-![BIDS-suggest-box](commenting_images/BIDS_suggest.png "BIDS-suggest")
-
-Once the button is clicked the highlighted text will be copied into the comment box and formatted as
-a [Markdown code block](https://help.github.com/en/github/writing-on-github/creating-and-highlighting-code-blocks).
-
-![BIDS-suggest-text](commenting_images/BIDS_suggest_text.png "BIDS-suggest-box")
-
-The "Preview" tab in the comment box will show your suggestion as it will be rendered.
-The "Suggested change" box will highlight the differences between the original text and your suggestion.
-
-![BIDS-suggest-change](commenting_images/BIDS_suggest_change.png "BIDS-suggest-change")
-
-A comment may be submitted on its own by clicking "Add single comment".
-Several comments may be grouped by clicking "Start a review".
-As more comments are written, accept them with "Add review comment", and submit your review comments
-as a batch by clicking the "Finish your review" button.
-
-## Writing in markdown
-
-The specification documents follow the [Markdown Style Guide](http://www.cirosantilli.com/markdown-style-guide/).
-
-You
-can validate your changes against the guide using [remark](https://github.com/remarkjs/remark-lint) which works as a
-[standalone command line tool](https://github.com/remarkjs/remark/tree/master/packages/remark-cli) as well as [a plugin for various text editors](https://github.com/remarkjs/remark-lint#editor-integrations). Remark preserves consistent markdown styling across the contributions. Please ensure before submitting a contribution that you do not have any linter errors in your text editor.
-You can also use [prettier](https://github.com/prettier/prettier) to automatically correct some of the style issues that might be found in the proposed changes.
-
-We have deployed a continuous integrator ([circle CI](https://circleci.com/)) to further allow for integrating changes continuously. The CI is testing that the changes are inline with our standard styling.
-
-GitHub has a helpful page on [getting started with writing and formatting on GitHub](https://help.github.com/articles/getting-started-with-writing-and-formatting-on-github).
-
-## Building the specification using mkdocs
-
-We are using mkdocs to render our specification. Please follow these instructions if you would like to build the specification locally.
-
-#### 1. Install mkdocs
-
-To begin please follow [this link](https://www.mkdocs.org/#installation) to install mkdocs locally.
-
-#### 2. Download the BIDS specification [repository](https://github.com/bids-standard/bids-specification/tree/master) onto your computer
-
-This can be done by clicking the green button on the right titled "Clone or download"
-
-#### 3. Install our theme
-
-Please go [here](https://squidfunk.github.io/mkdocs-material/) and install our theme - material. The terminal command is `pip install mkdocs-material`
-
-#### 4. In the terminal (command line) navigate to your local version of the specification
-
-This location will have the same files you see on our [main specification page](https://github.com/bids-standard/bids-specification). Note: A finder window may not show the hidden files (those that start with a period, like `.remarkrc`)
-
-#### 5. Ready to build!
-
-Using the terminal (command line) please enter `mkdocs serve`. This will allow you to see a local version of the specification. The local address will be `http://127.0.0.1:8000`. You may enter that into your browser and this will bring up the specification!
-
-## Making a change with a pull request
-
-We appreciate all contributions to the BIDS Specification. **THANK YOU** for helping us build this useful resource.
-
-#### 1. Comment on an existing issue or open a new issue referencing your addition
-
-This allows other members of the BIDS Specification team to confirm that you aren't overlapping with work that's currently underway and that everyone is on the same page with the goal of the work you're going to carry out.
-
-
-#### 2. [Fork](https://help.github.com/articles/fork-a-repo/) [this repository](https://github.com/bids-standard/bids-specification) to your profile
-
-This is now your own unique copy of the BIDS Specification. Changes here won't affect anyone else's work, so it's a safe space to explore edits to the specification!
-
-Make sure to [keep your fork up to date](https://help.github.com/articles/syncing-a-fork/) with the master repository, otherwise you can end up with lots of dreaded [merge conflicts](https://help.github.com/articles/about-merge-conflicts/).
-
-#### 3. Make the changes you've discussed
-
-Try to keep the changes focused. If you submit a large amount of work in all in one go it will be much more work for whomever is reviewing your pull request. Please detail the changes you are attempting to make.
-
-#### 4. Submit a [pull request](https://help.github.com/articles/about-pull-requests/)
-
-Please keep the title of your pull request short but informative - it will
-appear in the [changelog](src/CHANGES.md).
-
-Use one of the following prefixes in the title of your pull request:
-  - `[ENH]` - enhancement of the specification that adds a new feature or
-    support for a new data type
-  - `[FIX]` - fix of a typo or language clarification
-  - `[INFRA]` - changes to the infrastructure automating the specification
-    release (for example, building HTML docs)
-  - `[MISC]` - everything else including changes to the file listing
-    contributors
-
-If you are opening a pull request to obtain early feedback, but the changes
-are not ready to be merged (a.k.a. Work in Progress pull request) please
-use a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
-
-A member of the BIDS Specification team will review your changes to confirm that they can be merged into the main codebase.
-
-A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your GitHub notifications and be prepared to join in that conversation.
-
-You can update your [fork](https://help.github.com/articles/about-forks/) of the BIDS Specification and the pull request will automatically update with those commits. You don't need to submit a new pull request when you make a change in response to a review.
-
-GitHub has a [nice introduction](https://help.github.com/articles/github-flow/) to the pull request workflow, but please [get in touch](#get-in-touch) if you have any questions.
-
-## Example pull request
-<img align="center" src="https://i.imgur.com/s8yELfK.png" alt="Example-Contribution" width="800"/>
-
-
-## Updating the schema
-
-Portions of the BIDS specification are defined using YAML files, in order to make the specification machine-readable.
-Currently, the only portion of the specification that relies on this schema is the Entity Table, but any changes to the specification should be mirrored in the schema.
-
-### The format of the schema
-
-The schema reflects the files and objects in the specification, as well as associations between these objects.
-Here is a list of the files and subfolders of the schema, roughly in order of importance:
-
-- `datatypes/*.yaml`:
-    Data types supported by the specification.
-    Each datatype may support many suffixes.
-    These suffixes are divided into groups based on what extensions and entities are allowed for each.
-    Data types correspond to subfolders (for example, `anat`, `func`) in the BIDS structure.
-- `auxdatatypes/*.yaml`:
-    Auxiliary (not directly imaging or data-containing) data types supported by the specification.
-    Each auxiliary data type is associated with a set of data types, and these auxiliary data types are grouped based on what data types, extensions, and entities are allowed for each.
-    Examples of auxiliary data types include `channels`, `electrodes`, and `photo`.
-- `entities.yaml`:
-    A list of entities (key/value pairs in folder and filenames) with associated descriptions and formatting rules.
-    The order of the entities in the file determines the order in which entities must appear in filenames.
-- `top_level_files.yaml`:
-    Modality-agnostic files stored at the top level of a BIDS dataset.
-    The schema specifies whether these files are required or optional, as well as acceptable extensions for each.
-- `modalities.yaml`:
-    Modalities supported by the specification, along with a list of associated data types.
-    Modalities are not reflected directly in the BIDS structure, but data types are modality-specific.
-- `associated_data.yaml`:
-    Folders that are commonly contained within the same folder as a BIDS dataset, but which do not follow the BIDS structure internally, such as `code` or `sourcedata`.
-    The schema specifies which folders are accepted and whether they are required or optional.
-
-### Making a change to the schema
-
-#### 1. Ensure that changes to the specification are matched in the schema
-
-The schema formalizes the rules described in the specification text, so you must ensure that any changes which impact the rules of the specification (including, but not limited to, adding new entities, suffixes, datatypes, modalities) are reflected in the schema as well.
-
-#### 2. Generate an updated entity table before pushing your changes
-
-Run the Python script `tools/bids_schema.py`:
-
-```bash
-python tools/bids_schema.py entity src/schema/ src/99-appendices/04-entity-table.md
-```
-
-#### 3. Push your changes
-
-For more information on making general changes with a pull request, please review [Making a change with a pull request](#making-a-change-with-a-pull-request).
-
-## Fixing Travis Remark errors
-
-We use a linter called [Remarkjs](https://github.com/remarkjs/remark-lint) to ensure all of
-our Markdown documents are consistent and well-styled.
-This commonly produces errors, which are flagged by [Travis CI](https://travis-ci.org/),
-a continuous integration service.
-When Travis returns an error, use the following process to resolve the issue:
-
-#### 1. Install NodeJS / npm
-
-We use a markdown linter written in Javascript.
-To run command Javascript tools on the command line, please [download and
-install](https://nodejs.org/en/download/) NodeJS.
-
-#### 2. Install Remark-CLI and our style guide
-
-Remark-CLI can be installed via [npm](https://www.npmjs.com/), which is part of
-the NodeJS distribution.
-
-To install the packages we use for our style guide, the following command will work on most command lines:
-
-```
-npm install `cat npm-requirements.txt`
-```
-
-The equivalent command on PowerShell is:
-
-```
-npm install @(cat npm-requirements.txt)
-```
-
-#### 3. Fix the flagged document
-
-Please go to the directory where the flagged file is and run remark like this:
-
-```
-remark flagged_file.md -o flagged_file_fixed.md
-```
-
-Please confirm this has fixed the file.
-To do this, please run this:
-
-```
-remark flagged_file_fixed.md --frail
-```
-
-This command will indicate whether this file now conforms to the style guide.
-If it passes, replace `flagged_file.md` with the contents of `flagged_file_fixed.md`,
-add and commit the change:
-
-```
-mv flagged_file_fixed.md flagged_file.md
-git add flagged_file.md
-git commit -m 'STY: Fixed Markdown style'
-```
-
-## How the decision to merge a pull request is made?
-
-The decision-making rules are outlined in [DECISION-MAKING.md](DECISION-MAKING.md).
-
-
-## Recognizing contributions
-
-BIDS follows the [all-contributors](https://github.com/kentcdodds/all-contributors) specification, so we welcome and recognize all contributions from documentation to testing to code development. You can see a list of current contributors in the [BIDS specification](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md).
-
-## Thank you!
-
-You're awesome. 
-
-
--->
diff --git a/README.md b/README.md
index ab193907..681cf30e 100644
--- a/README.md
+++ b/README.md
@@ -35,7 +35,7 @@ This is a set of functions to MRI analysis on a
 
 ## Installation
 
-TODO
+<!-- TODO -->
 
 We strongly recommend using the CPP fMRI analysis template repository (INSERT
 URL) to use CPP_SPM.
@@ -114,6 +114,14 @@ Please see our
 [documentation](https://cpp-bids-spm.readthedocs.io/en/latest/index.html) for
 more info.
 
+## Octave compatibility
+
+The following features do not yet work with Octave:
+
+-   anatomicalQA
+-   functionalQA
+-   slice_display toolbox
+
 ## Contributing
 
 Feel free to open issues to report a bug and ask for improvements.
@@ -125,6 +133,18 @@ 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 guidelines
+
+These are some of the guidelines we try to follow.
+
+We use `camelCase` to name functions and variables for the vast majority of the
+code in this repository.
+
+Scripts names in general and as well functions related to the demos use a
+`snake_case`.
+
+Constant are written in `UPPERCASE`.
+
 ## Contributors
 
 Thanks goes to these wonderful people
diff --git a/demos/MoAE/dowload_MoAE_ds.m b/demos/MoAE/download_moae_ds.m
similarity index 90%
rename from demos/MoAE/dowload_MoAE_ds.m
rename to demos/MoAE/download_moae_ds.m
index f0be3cf9..03fc0621 100644
--- a/demos/MoAE/dowload_MoAE_ds.m
+++ b/demos/MoAE/download_moae_ds.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2021 Remi Gau
-
-function dowload_MoAE_ds(downloadData)
+function download_moae_ds(downloadData)
+  %
+  % (C) Copyright 2021 Remi Gau
 
   if downloadData
 
diff --git a/demos/MoAE/MoAE_create_roi_extract_data.m b/demos/MoAE/moae_create_roi_extract_data.m
similarity index 98%
rename from demos/MoAE/MoAE_create_roi_extract_data.m
rename to demos/MoAE/moae_create_roi_extract_data.m
index 22e0a5be..accf97bd 100644
--- a/demos/MoAE/MoAE_create_roi_extract_data.m
+++ b/demos/MoAE/moae_create_roi_extract_data.m
@@ -6,7 +6,7 @@
 % we are going to extract the value from.
 %
 
-run MoAE_run.m;
+run moae_run.m;
 
 subLabel = '01';
 
diff --git a/demos/MoAE/MoAE_getOption.m b/demos/MoAE/moae_get_option.m
similarity index 96%
rename from demos/MoAE/MoAE_getOption.m
rename to demos/MoAE/moae_get_option.m
index e36f9976..40110173 100644
--- a/demos/MoAE/MoAE_getOption.m
+++ b/demos/MoAE/moae_get_option.m
@@ -1,8 +1,9 @@
-% (C) Copyright 2019 Remi Gau
-
-function opt = MoAE_getOption()
+function opt = moae_get_option()
+  %
   % returns a structure that contains the options chosen by the user to run
   % slice timing correction, pre-processing, FFX, RFX.
+  %
+  % (C) Copyright 2019 Remi Gau
 
   opt = [];
 
diff --git a/demos/MoAE/MoAE_run.m b/demos/MoAE/moae_run.m
similarity index 80%
rename from demos/MoAE/MoAE_run.m
rename to demos/MoAE/moae_run.m
index bee7d73d..4d4d71b0 100644
--- a/demos/MoAE/MoAE_run.m
+++ b/demos/MoAE/moae_run.m
@@ -18,18 +18,17 @@
 run ../../initCppSpm.m;
 
 %% Set options
-opt = MoAE_getOption();
+opt = moae_get_option();
 
-dowload_MoAE_ds(downloadData);
+download_moae_ds(downloadData);
 
 %% Run batches
 reportBIDS(opt);
 bidsCopyRawFolder(opt, 1);
 
 % In case you just want to run segmentation and skull stripping
-
-bidsSegmentSkullStrip(opt);
-
+% bidsSegmentSkullStrip(opt);
+%
 % NOTE: skull stripping is also included in 'bidsSpatialPrepro'
 
 bidsSTC(opt);
@@ -37,13 +36,17 @@
 bidsSpatialPrepro(opt);
 
 % The following do not run on octave for now (because of spmup)
-% anatomicalQA(opt);
-% bidsResliceTpmToFunc(opt);
-% functionalQA(opt);
+anatomicalQA(opt);
+bidsResliceTpmToFunc(opt);
+functionalQA(opt);
 
 bidsSmoothing(FWHM, opt);
 
-% The following crash on Travis CI
+% The following crash on CI
+WD = pwd;
 bidsFFX('specifyAndEstimate', opt, FWHM);
+cd(WD);
 bidsFFX('contrasts', opt, FWHM);
+cd(WD);
 bidsResults(opt, FWHM);
+cd(WD);
diff --git a/demos/MoAE/MoAE_slice_display.m b/demos/MoAE/moae_slice_display.m
similarity index 96%
rename from demos/MoAE/MoAE_slice_display.m
rename to demos/MoAE/moae_slice_display.m
index bf370a0c..a0662caa 100644
--- a/demos/MoAE/MoAE_slice_display.m
+++ b/demos/MoAE/moae_slice_display.m
@@ -1,7 +1,6 @@
 % (C) Copyright 2021 Remi Gau
 
-run MoAE_run.m;
-run MoAE_create_roi_extract_data.m;
+run moae_create_roi_extract_data.m;
 
 close all;
 
diff --git a/demos/MoAE/options/options_task-auditory.json b/demos/MoAE/options/options_task-auditory.json
index 00982156..198477b0 100644
--- a/demos/MoAE/options/options_task-auditory.json
+++ b/demos/MoAE/options/options_task-auditory.json
@@ -1,19 +1,12 @@
 {
-    "STC_referenceSlice": [],
     "anatReference": {
         "type": "T1w",
-        "session": 1
+        "session": ""
     },
-    "contrastList": [],
-    "dataDir": "/home/remi/github/CPP_SPM/demos/MoAE/output/MoAEpilot",
-    "derivativesDir": "/home/remi/github/CPP_SPM/demos/MoAE/derivatives/default",
-    "funcVoxelDims": [],
-    "groups": [""],
+    "dataDir": "./inputs/raw",
+    "derivativesDir": "./outputs/",
     "model": {
-        "file": "/home/remi/github/CPP_SPM/demos/MoAE/models/model-MoAE_smdl.json"
-    },
-    "realign": {
-        "useUnwarp": true
+        "file": "./models/model-MoAE_smdl.json"
     },
     "result": {
         "Steps": {
@@ -41,9 +34,7 @@
     "skullstrip": {
         "threshold": 0.75
     },
-    "sliceOrder": [],
     "space": "MNI",
-    "subjects": [[]],
     "taskName": "auditory",
     "useFieldmaps": true,
     "zeropad": 2
diff --git a/demos/MoAE/options/options_task-auditory_space-individual.json b/demos/MoAE/options/options_task-auditory_space-individual.json
index 346b482b..4abd8a40 100644
--- a/demos/MoAE/options/options_task-auditory_space-individual.json
+++ b/demos/MoAE/options/options_task-auditory_space-individual.json
@@ -1,15 +1,12 @@
 {
-    "STC_referenceSlice": [],
     "anatReference": {
         "type": "T1w",
-        "session": 1
+        "session": ""
     },
-    "contrastList": [],
-    "dataDir": "/home/remi/github/CPP_SPM/demos/MoAE/output/MoAEpilot",
-    "derivativesDir": "/home/remi/github/CPP_SPM/demos/MoAE/derivatives/native",
-    "funcVoxelDims": [],
+    "dataDir": "./inputs/raw",
+    "derivativesDir": "./outputs/",
     "model": {
-        "file": "/home/remi/github/CPP_SPM/demos/MoAE/models/model-MoAE_smdl.json"
+        "file": "./models/model-MoAE_smdl.json"
     },
     "realign": {
         "useUnwarp": true
@@ -40,7 +37,6 @@
     "skullstrip": {
         "threshold": 0.75
     },
-    "sliceOrder": [],
     "space": "individual",
     "taskName": "auditory",
     "useFieldmaps": true,
diff --git a/demos/MoAE/options/options_task-auditory_unwarp-0.json b/demos/MoAE/options/options_task-auditory_unwarp-0.json
index 009b8147..8430077f 100644
--- a/demos/MoAE/options/options_task-auditory_unwarp-0.json
+++ b/demos/MoAE/options/options_task-auditory_unwarp-0.json
@@ -1,15 +1,12 @@
 {
-    "STC_referenceSlice": [],
     "anatReference": {
         "type": "T1w",
-        "session": 1
+        "session": ""
     },
-    "contrastList": [],
-    "dataDir": "/home/remi/github/CPP_SPM/demos/MoAE/output/MoAEpilot",
-    "derivativesDir": "/home/remi/github/CPP_SPM/demos/MoAE/derivatives/unwarp-0",
-    "funcVoxelDims": [],
+    "dataDir": "./inputs/raw",
+    "derivativesDir": "./outputs/",
     "model": {
-        "file": "/home/remi/github/CPP_SPM/demos/MoAE/models/model-MoAE_smdl.json"
+        "file": "./models/model-MoAE_smdl.json"
     },
     "realign": {
         "useUnwarp": false
@@ -40,7 +37,6 @@
     "skullstrip": {
         "threshold": 0.75
     },
-    "sliceOrder": [],
     "space": "MNI",
     "taskName": "auditory",
     "useFieldmaps": true,
diff --git a/demos/MoAE/options/options_task-auditory_unwarp-0_space-individual.json b/demos/MoAE/options/options_task-auditory_unwarp-0_space-individual.json
index 6dd7198f..2d1a17e5 100644
--- a/demos/MoAE/options/options_task-auditory_unwarp-0_space-individual.json
+++ b/demos/MoAE/options/options_task-auditory_unwarp-0_space-individual.json
@@ -1,15 +1,12 @@
 {
-    "STC_referenceSlice": [],
     "anatReference": {
         "type": "T1w",
-        "session": 1
+        "session": ""
     },
-    "contrastList": [],
-    "dataDir": "/home/remi/github/CPP_SPM/demos/MoAE/output/MoAEpilot",
-    "derivativesDir": "/home/remi/github/CPP_SPM/demos/MoAE/derivatives/unwarp-0_native",
-    "funcVoxelDims": [],
+    "dataDir": "./inputs/raw",
+    "derivativesDir": "./outputs/",
     "model": {
-        "file": "/home/remi/github/CPP_SPM/demos/MoAE/models/model-MoAE_smdl.json"
+        "file": "./models/model-MoAE_smdl.json"
     },
     "realign": {
         "useUnwarp": false
@@ -40,7 +37,6 @@
     "skullstrip": {
         "threshold": 0.75
     },
-    "sliceOrder": [],
     "space": "individual",
     "taskName": "auditory",
     "useFieldmaps": true,
diff --git a/demos/MoAE/return_normalized_anat_file.m b/demos/MoAE/return_normalized_anat_file.m
index b6a3627f..785543dc 100644
--- a/demos/MoAE/return_normalized_anat_file.m
+++ b/demos/MoAE/return_normalized_anat_file.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2021 Remi Gau
-
 function [anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel)
+  %
+  % (C) Copyright 2021 Remi Gau
 
   [BIDS, opt] = getData(opt);
   [~, anatDataDir] = getAnatFilename(BIDS, subLabel, opt);
diff --git a/demos/spm_face_rep/dowload_convert_face_rep_ds.m b/demos/face_repetition/download_convert_face_rep_ds.m
similarity index 98%
rename from demos/spm_face_rep/dowload_convert_face_rep_ds.m
rename to demos/face_repetition/download_convert_face_rep_ds.m
index a57bc975..72a901f7 100644
--- a/demos/spm_face_rep/dowload_convert_face_rep_ds.m
+++ b/demos/face_repetition/download_convert_face_rep_ds.m
@@ -1,12 +1,11 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
-function dowload_convert_face_rep_ds()
+function download_convert_face_rep_ds()
   %
-  % downloads the fare repetition dataset from SPM and convert it to BIDS
+  % downloads the face repetition dataset from SPM and convert it to BIDS
   %
   % Adapted from its counterpart for MoAE
   % <https://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAE_convert2bids.m>
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   subject = 'sub-01';
   task_name = 'face repetition';
diff --git a/demos/spm_face_rep/face_rep_anat.m b/demos/face_repetition/face_rep_anat.m
similarity index 79%
rename from demos/spm_face_rep/face_rep_anat.m
rename to demos/face_repetition/face_rep_anat.m
index 0df75713..eac2850b 100644
--- a/demos/spm_face_rep/face_rep_anat.m
+++ b/demos/face_repetition/face_rep_anat.m
@@ -1,7 +1,5 @@
 % (C) Copyright 2019 Remi Gau
-
-% This script will download the face repetition dataset from the FIL
-% and will run the basic preprocessing, FFX and contrasts on it.
+%
 %
 % This show how an anat only workflow would look like
 %
@@ -22,7 +20,7 @@
 %% Removes previous analysis, gets data and converts it to BIDS
 if downloadData
 
-  dowload_convert_face_rep_ds();
+  download_convert_face_rep_ds();
 
 end
 
diff --git a/demos/spm_face_rep/face_rep_func.m b/demos/face_repetition/face_rep_func.m
similarity index 94%
rename from demos/spm_face_rep/face_rep_func.m
rename to demos/face_repetition/face_rep_func.m
index 5a104a5b..b8817171 100644
--- a/demos/spm_face_rep/face_rep_func.m
+++ b/demos/face_repetition/face_rep_func.m
@@ -1,5 +1,5 @@
 % (C) Copyright 2019 Remi Gau
-
+%
 % This script will download the face repetition dataset from the FIL
 % and will run the basic preprocessing, FFX and contrasts on it.
 %
@@ -24,12 +24,12 @@
 run ../../initCppSpm.m;
 
 %% Set options
-opt = FaceRep_getOption();
+opt = face_rep_get_option();
 
 %% Removes previous analysis, gets data and converts it to BIDS
 if downloadData
 
-  dowload_convert_face_rep_ds();
+  download_convert_face_rep_ds();
 
 end
 
diff --git a/demos/spm_face_rep/FaceRep_getOption.m b/demos/face_repetition/face_rep_get_option.m
similarity index 85%
rename from demos/spm_face_rep/FaceRep_getOption.m
rename to demos/face_repetition/face_rep_get_option.m
index 660accd7..ea0293e3 100644
--- a/demos/spm_face_rep/FaceRep_getOption.m
+++ b/demos/face_repetition/face_rep_get_option.m
@@ -1,8 +1,9 @@
-% (C) Copyright 2020 Remi Gau
-
-function opt = FaceRep_getOption()
+function opt = face_rep_get_option()
+  %
   % returns a structure that contains the options chosen by the user to run
   % slice timing correction, pre-processing, FFX, RFX.
+  %
+  % (C) Copyright 2020 Remi Gau
 
   opt = [];
 
diff --git a/demos/spm_face_rep/FaceRep_getOptionResults.m b/demos/face_repetition/face_rep_get_option_results.m
similarity index 90%
rename from demos/spm_face_rep/FaceRep_getOptionResults.m
rename to demos/face_repetition/face_rep_get_option_results.m
index 541fc08a..8b36c80c 100644
--- a/demos/spm_face_rep/FaceRep_getOptionResults.m
+++ b/demos/face_repetition/face_rep_get_option_results.m
@@ -1,8 +1,8 @@
-% (C) Copyright 2021 Remi Gau
+function opt =  face_rep_get_option_results()
+  %
+  % (C) Copyright 2021 Remi Gau
 
-function opt =  FaceRep_getOptionResults()
-
-  opt = FaceRep_getOption();
+  opt = face_rep_get_option();
 
   opt.model.file = fullfile( ...
                             fileparts(mfilename('fullpath')), ...
diff --git a/demos/spm_face_rep/face_rep_resolution.m b/demos/face_repetition/face_rep_resolution.m
similarity index 84%
rename from demos/spm_face_rep/face_rep_resolution.m
rename to demos/face_repetition/face_rep_resolution.m
index 3e2ec99e..38461e17 100644
--- a/demos/spm_face_rep/face_rep_resolution.m
+++ b/demos/face_repetition/face_rep_resolution.m
@@ -1,6 +1,5 @@
 % (C) Copyright 2019 Remi Gau
-
-% adapted from face_rep_fun
+%
 %
 % runs preprocessing with different final spatial resolution in MNI space
 %
@@ -17,12 +16,12 @@
 
 %% Set options
 
-opt = FaceRep_getOptionResults();
+opt = face_rep_get_option_results();
 
 %% Removes previous analysis, gets data and converts it to BIDS
 if downloadData
 
-  dowload_convert_face_rep_ds();
+  download_convert_face_rep_ds();
 
 end
 
@@ -42,6 +41,10 @@
                                          'derivatives', ...
                                          ['cpp_spm-res' num2str(iResolution)]), 'cpath');
 
+  % create a new BIDS model json file
+  % this way the GLM output will be store in a different directory for each
+  % resolution as the name of the GLM directory is based on the name of the
+  % model in the BIDS model
   content = spm_jsonread(opt.model.file);
   content.Name = [content.Name, ' resolution - ', num2str(iResolution)];
 
@@ -52,6 +55,7 @@
 
   spm_jsonwrite(newModel, content, struct('indent', '   '));
 
+  % run analysis
   bidsCopyRawFolder(opt, 1);
 
   bidsSTC(opt);
diff --git a/demos/spm_face_rep/face_rep_roi_analysis.m b/demos/face_repetition/face_rep_roi_analysis.m
similarity index 92%
rename from demos/spm_face_rep/face_rep_roi_analysis.m
rename to demos/face_repetition/face_rep_roi_analysis.m
index dc8b8af3..4799bd3c 100644
--- a/demos/spm_face_rep/face_rep_roi_analysis.m
+++ b/demos/face_repetition/face_rep_roi_analysis.m
@@ -1,11 +1,12 @@
 % (C) Copyright 2019 Remi Gau
-
+%
 % creates a ROI in MNI space from the proba atlas
 % creates its equivalent in subject space
+%
 
 run face_rep_anat.m;
 
-opt = FaceRep_getOption();
+opt = face_rep_get_option();
 
 opt.roi.atlas = 'wang';
 opt.roi.name = {'V1v', 'V1d'};
diff --git a/demos/spm_face_rep/models/model-faceRepetition_smdl.json b/demos/face_repetition/models/model-faceRepetition_smdl.json
similarity index 100%
rename from demos/spm_face_rep/models/model-faceRepetition_smdl.json
rename to demos/face_repetition/models/model-faceRepetition_smdl.json
diff --git a/demos/lesiondetection/batchLesion.m b/demos/lesion_detection/batch_lesion.m
similarity index 85%
rename from demos/lesiondetection/batchLesion.m
rename to demos/lesion_detection/batch_lesion.m
index 7e66dc7c..87de2b2b 100644
--- a/demos/lesiondetection/batchLesion.m
+++ b/demos/lesion_detection/batch_lesion.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2021 CPP_SPM developers
 
 clear;
 clc;
diff --git a/demos/lesiondetection/Lesion_getOption.m b/demos/lesion_detection/lesion_get_option.m
similarity index 81%
rename from demos/lesiondetection/Lesion_getOption.m
rename to demos/lesion_detection/lesion_get_option.m
index 04e97c78..2da9718f 100644
--- a/demos/lesiondetection/Lesion_getOption.m
+++ b/demos/lesion_detection/lesion_get_option.m
@@ -1,6 +1,4 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
-function opt = Lesion_getOption()
+function opt = lesion_get_option()
   %
   % Returns a structure that contains the options chosen by the user to run the source processing
   % batch workflow
@@ -10,6 +8,8 @@
   %  opt = Lesion_getOption()
   %
   % :returns: - :optSource: (struct)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   % The directory where the data are located
   opt.dataDir = '/home/remi/gin/CVI-Datalad/data';
diff --git a/demos/miss_hit.cfg b/demos/miss_hit.cfg
index 25947f2d..007bd432 100644
--- a/demos/miss_hit.cfg
+++ b/demos/miss_hit.cfg
@@ -1,12 +1 @@
-# styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
-line_length: 100
-regex_function_name: "[a-zA-Z0-9]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*" # almost anything goes in the root folder
-copyright_entity: "Mohamed Rezk"
-copyright_entity: "Remi Gau"
-copyright_entity: "CPP BIDS SPM-pipeline developpers"
-
-# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
-metric "cnest": limit 4
-metric "file_length": limit 400
-metric "cyc": limit 12
-metric "parameters": limit 6
\ No newline at end of file
+regex_function_name: "[a-z0-9]+(_[a-z0-9]+)*"
\ No newline at end of file
diff --git a/demos/openneuro/ds000001_getOption.m b/demos/openneuro/ds000001_get_option.m
similarity index 93%
rename from demos/openneuro/ds000001_getOption.m
rename to demos/openneuro/ds000001_get_option.m
index b468ef5b..8d9daa1b 100644
--- a/demos/openneuro/ds000001_getOption.m
+++ b/demos/openneuro/ds000001_get_option.m
@@ -1,8 +1,9 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
-function opt = ds000001_getOption()
+function opt = ds000001_get_option()
+  %
   % returns a structure that contains the options chosen by the user to run
   % slice timing correction, pre-processing, FFX, RFX.
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 1
     opt = [];
diff --git a/demos/openneuro/ds000001_run.m b/demos/openneuro/ds000001_run.m
index 8e1ce6fc..a0d11fab 100644
--- a/demos/openneuro/ds000001_run.m
+++ b/demos/openneuro/ds000001_run.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 % runDs00014
 
@@ -12,7 +12,7 @@
 run ../../initCppSpm.m;
 
 %% Set options
-opt = ds000001_getOption();
+opt = ds000001_get_option();
 
 reportBIDS(opt);
 
diff --git a/demos/openneuro/ds000114_getOption.m b/demos/openneuro/ds000114_get_option.m
similarity index 94%
rename from demos/openneuro/ds000114_getOption.m
rename to demos/openneuro/ds000114_get_option.m
index 5797314e..caf9fd1c 100644
--- a/demos/openneuro/ds000114_getOption.m
+++ b/demos/openneuro/ds000114_get_option.m
@@ -1,8 +1,10 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
-function opt = ds000114_getOption()
+function opt = ds000114_get_option()
+  %
   % returns a structure that contains the options chosen by the user to run
   % slice timing correction, pre-processing, FFX, RFX.
+  %
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 1
     opt = [];
diff --git a/demos/openneuro/ds000114_run.m b/demos/openneuro/ds000114_run.m
index 56f61cfd..f3d8dd1d 100644
--- a/demos/openneuro/ds000114_run.m
+++ b/demos/openneuro/ds000114_run.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 % runDs00014
 
@@ -12,7 +12,7 @@
 run ../../initCppSpm.m;
 
 %% Set options
-opt = ds000114_getOption();
+opt = ds000114_get_option();
 
 %% Run batches
 
diff --git a/demos/openneuro/ds001168_getOption.m b/demos/openneuro/ds001168_get_option.m
similarity index 88%
rename from demos/openneuro/ds001168_getOption.m
rename to demos/openneuro/ds001168_get_option.m
index 6a6ebfb4..ce65ee10 100644
--- a/demos/openneuro/ds001168_getOption.m
+++ b/demos/openneuro/ds001168_get_option.m
@@ -1,8 +1,10 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
-function opt = ds001168_getOption()
+function opt = ds001168_get_option()
+  %
   % returns a structure that contains the options chosen by the user to run
   % slice timing correction, pre-processing, FFX, RFX.
+  %
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 1
     opt = [];
diff --git a/demos/openneuro/ds001168_run.m b/demos/openneuro/ds001168_run.m
index 701c88c1..695b3b6d 100644
--- a/demos/openneuro/ds001168_run.m
+++ b/demos/openneuro/ds001168_run.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 % runDs001168
 
@@ -11,7 +11,7 @@
 run ../../initCppSpm.m;
 
 %% Set options
-opt = ds001168_getOption();
+opt = ds001168_get_option();
 
 %% Run batches
 
diff --git a/demos/vismotion/batch.m b/demos/vismotion/batch.m
index ce2ef814..b88ef07b 100644
--- a/demos/vismotion/batch.m
+++ b/demos/vismotion/batch.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2019 CPP_SPM developers
 
 clear;
 clc;
@@ -9,7 +9,7 @@
 run ../../initCppSpm.m;
 
 %% Run batches
-opt = getOption();
+opt = get_option();
 
 reportBIDS(opt);
 
diff --git a/demos/vismotion/getOption.m b/demos/vismotion/get_option.m
similarity index 84%
rename from demos/vismotion/getOption.m
rename to demos/vismotion/get_option.m
index dca50692..1671e4f7 100644
--- a/demos/vismotion/getOption.m
+++ b/demos/vismotion/get_option.m
@@ -1,9 +1,11 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
-function opt = getOption()
-  % opt = getOption()
+function opt = get_option()
+  %
   % returns a structure that contains the options chosen by the user to run
   % slice timing correction, pre-processing, FFX, RFX.
+  %
+  % opt = get_option()
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   if nargin < 1
     opt = [];
@@ -17,8 +19,7 @@
   opt.derivativesDir = '/home/remi/Documents';
 
   % specify the model file that contains the contrasts to compute
-  opt.model.file = ...
-      '/home/remi/github/CPP_BIDS_SPM_pipeline/demos/vismotion/models/model-visMotionLoc_smdl.json';
+  opt.model.file = './vismotion/models/model-visMotionLoc_smdl.json';
 
   % specify the result to compute
   % Contrasts.Name has to match one of the contrast defined in the model json file
diff --git a/docs/README.md b/docs/README.md
index 4f1ca4e7..add9f199 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -3,8 +3,8 @@
 ## Set up virtual environment
 
 ```bash
-virtualenv -p python3 cpp_spm
-source cpp_spm/bin/activate
+virtualenv -p /usr/bin/python3 env
+source env/bin/activate
 
 pip install -r requirements.txt
 ```
diff --git a/docs/source/batches.rst b/docs/source/batches.rst
index 9da85ccb..86076033 100644
--- a/docs/source/batches.rst
+++ b/docs/source/batches.rst
@@ -7,25 +7,35 @@ List of functions to set SPM batches.
 
 .. automodule:: src.batches
 
+.. autofunction:: setBatch3Dto4D
 .. autofunction:: setBatchComputeVDM
+.. autofunction:: setBatchContrasts
 .. autofunction:: setBatchCoregistrationFmap
 .. autofunction:: setBatchCoregistrationFuncToAnat
 .. autofunction:: setBatchCoregistration
 .. autofunction:: setBatchCreateVDMs
+.. autofunction:: setBatchEstimateModel
 .. autofunction:: setBatchFactorialDesign
+.. autofunction:: setBatchGroupLevelContrasts
 .. autofunction:: setBatchImageCalculation
+.. autofunction:: setBatchLesionAbnormalitiesDetection
+.. autofunction:: setBatchLesionOverlapMap
+.. autofunction:: setBatchLesionSegmentation
 .. autofunction:: setBatchMeanAnatAndMask
 .. autofunction:: setBatchNormalizationSpatialPrepro
 .. autofunction:: setBatchNormalize
+.. autofunction:: setBatchPrintFigure
 .. autofunction:: setBatchRealign
 .. autofunction:: setBatchReslice
+.. autofunction:: setBatchResults
 .. autofunction:: setBatchSaveCoregistrationMatrix
 .. autofunction:: setBatchSegmentation
 .. autofunction:: setBatchSelectAnat
 .. autofunction:: setBatchSkullStripping
 .. autofunction:: setBatchSmoothConImages
+.. autofunction:: setBatchSmoothingFunc
 .. autofunction:: setBatchSmoothing
 .. autofunction:: setBatchSTC
 .. autofunction:: setBatchSubjectLevelContrasts
-.. autofunction:: setBatchSubjectLevelGLMSpec 
-   
\ No newline at end of file
+.. autofunction:: setBatchSubjectLevelGLMSpec
+.. autofunction:: setBatchSubjectLevelResults
\ No newline at end of file
diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
index d9855ed0..de47e77f 100644
--- a/docs/source/contributing.rst
+++ b/docs/source/contributing.rst
@@ -47,38 +47,6 @@ Template proposal
 .. autofunction:: templateFunction  
 
 
-----
-
-Numpy template
---------------
-
-See more information `here 
-<https://www.sphinx-doc.org/en/master/usage/extensions/example_numpy.html#example-numpy>`_
-
-::
-
-   function [argout] = templateFunction(argin1, argin2, argin3)
-      %
-      % Short description of what the function does goes here.
-      %
-      %  y = templateFunction(argin1, argin2, argin3)
-      %
-      % Parameters:
-      %    argin1: The first input value
-      %
-      %    argin2: The second input value
-      %
-      %    argin3: The third input value 
-      %
-      % Returns:
-      %    The output value
-
-      % The code goes below
-
-   end
-
-.. autofunction:: templateFunctionNumpy
-
 ----
 
 Google template
diff --git a/docs/source/demos.rst b/docs/source/demos.rst
new file mode 100644
index 00000000..31b2d9e4
--- /dev/null
+++ b/docs/source/demos.rst
@@ -0,0 +1,11 @@
+Demos
+=====
+
+::
+
+    demos/
+    ├── face_repetition
+    ├── lesion_detection
+    ├── MoAE
+    ├── openneuro
+    └── vismotion
\ No newline at end of file
diff --git a/docs/source/function_description.rst b/docs/source/function_description.rst
index 10745525..efa37956 100644
--- a/docs/source/function_description.rst
+++ b/docs/source/function_description.rst
@@ -16,7 +16,6 @@ List of functions in the ``src`` folder.
 .. autofunction:: getPrefix
 .. autofunction:: getRealignParamFile
 .. autofunction:: getSliceOrder
-.. autofunction:: getSpecificSubjects
 .. autofunction:: setDerivativesDir
 .. autofunction:: unzipImgAndReturnsFullpathName
 
@@ -25,7 +24,6 @@ Subject level model
 
 .. automodule:: src.subject_level
 
-.. autofunction:: concatBetaImgTmaps
 .. autofunction:: convertOnsetTsvToMat
 .. autofunction:: createAndReturnOnsetFile
 .. autofunction:: deleteResidualImages
@@ -62,15 +60,26 @@ Utility functions
 .. automodule:: src.utils 
 
 .. autofunction:: checkDependencies
+.. autofunction:: cleanCrash
 .. autofunction:: createDataDictionary
+.. autofunction:: createDerivativeDir
+.. autofunction:: createGlmDirName
 .. autofunction:: getEnvInfo
+.. autofunction:: getSubjectList
 .. autofunction:: getVersion
 .. autofunction:: isOctave
 .. autofunction:: loadAndCheckOptions
+.. autofunction:: manageWorkersPool
+.. autofunction:: printBatchName
 .. autofunction:: printCredits
 .. autofunction:: printProcessingRun
 .. autofunction:: printProcessingSubject
+.. autofunction:: printWorklowName
+.. autofunction:: removeSpmPrefix
+.. autofunction:: rmTrialTypeStr
 .. autofunction:: saveMatlabBatch
 .. autofunction:: saveOptions
-.. autofunction:: setDefaultFields
+.. autofunction:: setFields
+.. autofunction:: setGraphicWindow
 .. autofunction:: validationInputFile
+.. autofunction:: writeDatasetDescription
\ No newline at end of file
diff --git a/docs/source/index.rst b/docs/source/index.rst
index aafb80c3..5c2de617 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -11,10 +11,11 @@ Welcome to CPP SPM BIDS pipeline documentation!
    :caption: Content
 
    set_up
-   workflows
-   QA
    defaults
+   demos
+   workflows
    batches
+   QA
    function_description
    method_section_boilerplate
    mancoreg
@@ -22,7 +23,7 @@ Welcome to CPP SPM BIDS pipeline documentation!
    contributing
 
 This pipeline contains a set of functions to run fMRI analysis on a
-[BIDS data set](https://bids.neuroimaging.io/) using SPM12.
+`BIDS data set <https://bids.neuroimaging.io/>`_ using SPM12.
 
 This can perform:
 
diff --git a/docs/source/mancoreg.rst b/docs/source/mancoreg.rst
index 5dacf6f9..1460a2a6 100644
--- a/docs/source/mancoreg.rst
+++ b/docs/source/mancoreg.rst
@@ -5,7 +5,7 @@ Manual coregistration tools
 
 ----
 
-.. automodule:: src.mancoreg
+.. automodule:: lib.mancoreg
 
 .. autofunction:: mancoreg
 .. autofunction:: mancoregCallbacks
diff --git a/docs/source/workflows.rst b/docs/source/workflows.rst
index 06ffadd8..29cfe6d0 100644
--- a/docs/source/workflows.rst
+++ b/docs/source/workflows.rst
@@ -103,6 +103,13 @@ Compute results
 ===============
 
 .. autofunction:: bidsResults
+.. autofunction:: bidsConcatBetaTmaps    
+
+Region of interest analysis
+===========================
+
+.. autofunction::  bidsRoiBasedGLM
+.. autofunction::  bidsCreateROI
 
 Other
 =====
diff --git a/initCppSpm.m b/initCppSpm.m
index c4bdd80f..0ef52513 100644
--- a/initCppSpm.m
+++ b/initCppSpm.m
@@ -1,6 +1,8 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function initCppSpm()
+  %
+  % adds the relevant folders to the path
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   global CPP_SPM_INITIALIZED
 
diff --git a/manualTests/miss_hit.cfg b/manualTests/miss_hit.cfg
new file mode 100644
index 00000000..684e5239
--- /dev/null
+++ b/manualTests/miss_hit.cfg
@@ -0,0 +1 @@
+regex_function_name: "(test(_unit){0,1}_[a-z]+|[a-z]+)(([A-Z]){1}[A-Za-z0-9]+)*"
diff --git a/manualTests/test_bidsSegmentSkullStrip.m b/manualTests/test_bidsSegmentSkullStrip.m
deleted file mode 100644
index f10ea4b2..00000000
--- a/manualTests/test_bidsSegmentSkullStrip.m
+++ /dev/null
@@ -1,29 +0,0 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
-function test_suite = test_bidsSegmentSkullStrip %#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_bidsSegmentSkullStripBasic()
-
-  % smoke test
-
-  % directory with this script becomes the current directory
-  opt.dataDir = fullfile( ...
-                         fileparts(mfilename('fullpath')), ...
-                         '..', 'demos',  'MoAE', 'output', 'MoAEpilot');
-  % task to analyze
-  opt.taskName = 'auditory';
-  opt = checkOptions(opt);
-
-  %% Run batches
-  checkDependencies();
-  reportBIDS(opt);
-  bidsCopyRawFolder(opt, 1);
-  bidsSegmentSkullStrip(opt);
-
-end
diff --git a/manualTests/systemTestDS114.m b/manualTests/test_ds114.m
similarity index 99%
rename from manualTests/systemTestDS114.m
rename to manualTests/test_ds114.m
index b9dfb487..b9c18231 100644
--- a/manualTests/systemTestDS114.m
+++ b/manualTests/test_ds114.m
@@ -1,5 +1,5 @@
 % (C) Copyright 2019 Remi Gau
-
+%
 % Script to run to check that the whole pipeline works fine with different
 % options encoded in json files
 %
diff --git a/manualTests/systemTestMoAE.m b/manualTests/test_moae.m
similarity index 65%
rename from manualTests/systemTestMoAE.m
rename to manualTests/test_moae.m
index a2b87437..62892cd9 100644
--- a/manualTests/systemTestMoAE.m
+++ b/manualTests/test_moae.m
@@ -1,5 +1,5 @@
 % (C) Copyright 2019 Remi Gau
-
+%
 % Script to run to check that the whole pipeline works fine with different
 % options encoded in json files
 %
@@ -17,6 +17,8 @@
 % Smoothing to apply
 FWHM = 6;
 
+downloadData = true;
+
 % URL of the data set to download
 URL = 'http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip';
 
@@ -24,24 +26,11 @@
 WD = fullfile(fileparts(mfilename('fullpath')), '..', 'demos', 'MoAE');
 cd(WD);
 
-% we add all the subfunctions that are in the sub directories
-addpath(genpath(fullfile(WD, '..', '..', 'src')));
-addpath(genpath(fullfile(WD, '..', '..', 'lib')));
-
-%% Get data
-fprintf('%-10s:', 'Downloading dataset...');
-urlwrite(URL, 'MoAEpilot.zip');
-fprintf(1, ' Done\n\n');
-
-fprintf('%-10s:', 'Unzipping dataset...');
-unzip('MoAEpilot.zip', fullfile(WD, 'output'));
-fprintf(1, ' Done\n\n');
+run ../../initCppSpm.m;
 
-checkDependencies();
+dowload_moae_ds(downloadData);
 
 %% Set up
-delete(fullfile(pwd, 'options_task-*date-*.json'));
-
 optionsFilesList = { ...
                     'options_task-auditory.json'; ...
                     'options_task-auditory_unwarp-0.json'; ...
@@ -53,7 +42,7 @@
 
   fprintf(1, repmat('\n', 1, 5));
 
-  optionJsonFile = optionsFilesList{iOption};
+  optionJsonFile = fullfile(WD, 'options', optionsFilesList{iOption});
   opt = loadAndCheckOptions(optionJsonFile);
 
   %% Run batches
@@ -66,17 +55,23 @@
 
   bidsSpatialPrepro(opt);
 
-  % The following do not run on octave for now (because of spmup)
-  anatomicalQA(opt);
+  % Some of the following do not run on octave for now (because of spmup)
+  % Crashes in CI
+  %   anatomicalQA(opt);
+
   bidsResliceTpmToFunc(opt);
-  functionalQA(opt);
+
+  % Crashes in CI
+  %   functionalQA(opt);
 
   bidsSmoothing(FWHM, opt);
 
+  bidsSegmentSkullStrip(opt);
+
   % The following crash on Travis CI
-  bidsFFX('specifyAndEstimate', opt, FWHM);
-  bidsFFX('contrasts', opt, FWHM);
-  bidsResults(opt, FWHM);
+  %   bidsFFX('specifyAndEstimate', opt, FWHM);
+  %   bidsFFX('contrasts', opt, FWHM);
+  %   bidsResults(opt, FWHM);
 
   cd(WD);
 
diff --git a/manualTests/test_setBatchCoregistrationFmap.m b/manualTests/test_setBatchCoregistrationFmap.m
index eaa1f88c..4d055052 100644
--- a/manualTests/test_setBatchCoregistrationFmap.m
+++ b/manualTests/test_setBatchCoregistrationFmap.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchCoregistrationFmap %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/manualTests/test_setBatchCreateVDMs.m b/manualTests/test_setBatchCreateVDMs.m
index 314008e5..e87e6350 100644
--- a/manualTests/test_setBatchCreateVDMs.m
+++ b/manualTests/test_setBatchCreateVDMs.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchCreateVDMs %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/miss_hit.cfg b/miss_hit.cfg
index bce4b86c..3c2173ce 100644
--- a/miss_hit.cfg
+++ b/miss_hit.cfg
@@ -1,14 +1,18 @@
 # styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
-regex_function_name: "[a-z]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*"
+
+regex_function_name: "[a-z]+([a-zA-Z0-9]){1}[a-zA-Z0-9]+"
+regex_script_name: "[a-z0-9]+(_[a-z0-9]+)*"
+
 exclude_dir: "lib"
+
 copyright_entity: "JH"
 copyright_entity: "DSS"
 copyright_entity: "Agah Karakuzu"
 copyright_entity: "Olivier Collignon"
 copyright_entity: "Mohamed Rezk"
 copyright_entity: "Remi Gau"
-copyright_entity: "CPP BIDS SPM-pipeline developers"
+copyright_entity: "CPP_SPM developers"
 
 tab_width: 2
 
diff --git a/npm-requirements.txt b/npm-requirements.txt
deleted file mode 100644
index 061f9ade..00000000
--- a/npm-requirements.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-remark-cli@5.0.0
-remark-lint@6.0.2
-remark-preset-lint-recommended@3.0.2
-remark-preset-lint-markdown-style-guide@2.1.2
-remark-preset-lint-consistent
-
diff --git a/requirements.txt b/requirements.txt
index 992d0ece..578e596a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,4 +2,4 @@ Sphinx
 sphinxcontrib-matlabdomain
 sphinxcontrib-napoleon
 sphinx_rtd_theme
-miss_hit==0.9.15
\ No newline at end of file
+miss_hit==0.9.20
\ No newline at end of file
diff --git a/runTests.m b/run_tests.m
similarity index 91%
rename from runTests.m
rename to run_tests.m
index f1e02a48..98dc6821 100644
--- a/runTests.m
+++ b/run_tests.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2019 CPP_SPM developers
 
 warning('OFF');
 
diff --git a/src/QA/anatomicalQA.m b/src/QA/anatomicalQA.m
index c147602d..3e689e8c 100644
--- a/src/QA/anatomicalQA.m
+++ b/src/QA/anatomicalQA.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function anatomicalQA(opt)
   %
   % Computes several metrics for anatomical image.
@@ -11,6 +9,7 @@ function anatomicalQA(opt)
   % :param opt: Options chosen for the analysis. See ``checkOptions()``.
   % :type opt: structure
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if isOctave()
     warning('\nanatomicalQA is not yet supported on Octave. This step will be skipped.');
diff --git a/src/QA/functionalQA.m b/src/QA/functionalQA.m
index fa356499..f74ff38c 100644
--- a/src/QA/functionalQA.m
+++ b/src/QA/functionalQA.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function functionalQA(opt)
   %
   % For functional data, QA consists in getting temporal SNR and then
@@ -23,6 +21,8 @@ function functionalQA(opt)
   %   - the tissue probability maps have been generated in the "native" space of each subject
   %     (using ``bidsSpatialPrepro()`` or ``bidsSegmentSkullStrip()``) and have been
   %     resliced to the dimension of the functional with ``bidsResliceTpmToFunc()``
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if isOctave()
     warning('\nfunctionalQA is not yet supported on Octave. This step will be skipped.');
diff --git a/src/batches/setBatch3Dto4D.m b/src/batches/setBatch3Dto4D.m
index 90e761bb..d9811282 100644
--- a/src/batches/setBatch3Dto4D.m
+++ b/src/batches/setBatch3Dto4D.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatch3Dto4D(matlabbatch, volumesList, RT, outputName, dataType)
   %
   % Set the batch for 3D to 4D conversion
@@ -31,6 +29,7 @@
   %   - 16: FLOAT32 - single prec. float
   %   - 64: FLOAT64 - double prec. float
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 5 || isempty(dataType)
     dataType = 0;
diff --git a/src/batches/setBatchComputeVDM.m b/src/batches/setBatchComputeVDM.m
index 00321ae4..dddf02bb 100644
--- a/src/batches/setBatchComputeVDM.m
+++ b/src/batches/setBatchComputeVDM.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchComputeVDM(matlabbatch, fmapType, refImage)
   %
   % Short description of what the function does goes here.
@@ -21,6 +19,8 @@
   %
   % adapted from spmup get_FM_workflow.m (@ commit
   % 198c980d6d7520b1a996f0e56269e2ceab72cc83)
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   switch lower(fmapType)
     case 'phasediff'
diff --git a/src/batches/setBatchContrasts.m b/src/batches/setBatchContrasts.m
index ea047235..89162fe7 100644
--- a/src/batches/setBatchContrasts.m
+++ b/src/batches/setBatchContrasts.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchContrasts(matlabbatch, spmMatFile, consess)
   %
   % Short description of what the function does goes here.
@@ -17,6 +15,7 @@
   %
   % :returns: - :matlabbatch: (structure)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   printBatchName('contrasts specification');
 
diff --git a/src/batches/setBatchCoregistration.m b/src/batches/setBatchCoregistration.m
index 8fb4d51f..5efa1477 100644
--- a/src/batches/setBatchCoregistration.m
+++ b/src/batches/setBatchCoregistration.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchCoregistration(matlabbatch, ref, src, other)
   %
   % Set the batch for coregistering the source images into the reference image
@@ -21,6 +19,7 @@
   %
   % matlabbatch = setBatchCoregistrationGeneral(matlabbatch, ref, src, other)
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('coregistration');
 
diff --git a/src/batches/setBatchCoregistrationFmap.m b/src/batches/setBatchCoregistrationFmap.m
index cdf5ab90..2d1bcab7 100644
--- a/src/batches/setBatchCoregistrationFmap.m
+++ b/src/batches/setBatchCoregistrationFmap.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchCoregistrationFmap(matlabbatch, BIDS, opt, subLabel)
   %
   % Set the batch for the coregistration of field maps
@@ -18,9 +16,10 @@
   %
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
   %
-
   % TODO
   % - implement for 'phase12', 'fieldmap', 'epi'
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('coregister fieldmaps data to functional');
 
diff --git a/src/batches/setBatchCoregistrationFuncToAnat.m b/src/batches/setBatchCoregistrationFuncToAnat.m
index b9bc7dfa..70b4761a 100644
--- a/src/batches/setBatchCoregistrationFuncToAnat.m
+++ b/src/batches/setBatchCoregistrationFuncToAnat.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchCoregistrationFuncToAnat(matlabbatch, BIDS, opt, subLabel)
   %
   % Set the batch for corregistering the functional images to the
@@ -21,17 +19,18 @@
   %
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('coregister functional data to anatomical');
 
   matlabbatch{end + 1}.spm.spatial.coreg.estimate.ref(1) = ...
-      cfg_dep('Named File Selector: Anatomical(1) - Files', ...
-              substruct( ...
-                        '.', 'val', '{}', {opt.orderBatches.selectAnat}, ...
-                        '.', 'val', '{}', {1}, ...
-                        '.', 'val', '{}', {1}, ...
-                        '.', 'val', '{}', {1}), ...
-              substruct('.', 'files', '{}', {1}));
+   cfg_dep('Named File Selector: Anatomical(1) - Files', ...
+           substruct( ...
+                     '.', 'val', '{}', {opt.orderBatches.selectAnat}, ...
+                     '.', 'val', '{}', {1}, ...
+                     '.', 'val', '{}', {1}, ...
+                     '.', 'val', '{}', {1}), ...
+           substruct('.', 'files', '{}', {1}));
 
   % SOURCE IMAGE : DEPENDENCY FROM REALIGNEMENT
   % Mean Image
diff --git a/src/batches/setBatchCreateVDMs.m b/src/batches/setBatchCreateVDMs.m
index 54f4a08e..9851ed7f 100644
--- a/src/batches/setBatchCreateVDMs.m
+++ b/src/batches/setBatchCreateVDMs.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchCreateVDMs(matlabbatch, BIDS, opt, subID)
   %
   % Short description of what the function does goes here.
@@ -22,6 +20,8 @@
   %
   % TODO
   % - implement for 'phase12', 'fieldmap', 'epi'
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('create voxel displacement map');
 
diff --git a/src/batches/setBatchEstimateModel.m b/src/batches/setBatchEstimateModel.m
index 719e284e..de0ff6bf 100644
--- a/src/batches/setBatchEstimateModel.m
+++ b/src/batches/setBatchEstimateModel.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchEstimateModel(matlabbatch, opt, grpLvlCon)
   %
   % Short description of what the function does goes here.
@@ -15,6 +13,7 @@
   %
   % :returns: - :matlabbatch: (structure)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   switch nargin
 
diff --git a/src/batches/setBatchFactorialDesign.m b/src/batches/setBatchFactorialDesign.m
index ec5c9262..c063e68b 100644
--- a/src/batches/setBatchFactorialDesign.m
+++ b/src/batches/setBatchFactorialDesign.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchFactorialDesign(matlabbatch, opt, funcFWHM, conFWHM)
   %
   % Short description of what the function does goes here.
@@ -19,6 +17,7 @@
   %
   % :returns: - :matlabbatch: (structure)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   printBatchName('specify group level fmri model');
 
diff --git a/src/batches/setBatchGroupLevelContrasts.m b/src/batches/setBatchGroupLevelContrasts.m
index 5d83966c..f6346c4c 100644
--- a/src/batches/setBatchGroupLevelContrasts.m
+++ b/src/batches/setBatchGroupLevelContrasts.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchGroupLevelContrasts(matlabbatch, grpLvlCon, rfxDir)
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   printBatchName('group level contrast estimation');
 
diff --git a/src/batches/setBatchImageCalculation.m b/src/batches/setBatchImageCalculation.m
index 771aee1e..e350d6b6 100644
--- a/src/batches/setBatchImageCalculation.m
+++ b/src/batches/setBatchImageCalculation.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchImageCalculation(matlabbatch, input, output, outDir, expression)
   %
   % Set a batch for a image calculation
@@ -21,6 +19,7 @@
   %
   % :returns: - :matlabbatch:
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('image calculation');
 
diff --git a/src/batches/setBatchLesionAbnormalitiesDetection.m b/src/batches/setBatchLesionAbnormalitiesDetection.m
index cf906292..8ea61493 100755
--- a/src/batches/setBatchLesionAbnormalitiesDetection.m
+++ b/src/batches/setBatchLesionAbnormalitiesDetection.m
@@ -1,17 +1,17 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
-function matlabbatch = setBatchLesionAbnormalities(matlabbatch, BIDS, opt, subLabel)
+function matlabbatch = setBatchLesionAbnormalitiesDetection(matlabbatch, BIDS, opt, subLabel)
   %
   % Creates a batch to detect lesion abnormalities
   %
   % USAGE::
   %
-  %   matlabbatch = setBatchLesionAbnormalities(matlabbatch, BIDS, opt, subLabel)
+  %   matlabbatch = setBatchLesionAbnormalitiesDetection(matlabbatch, BIDS, opt, subLabel)
   %
   % :param matlabbatch: list of SPM batches
   % :type matlabbatch: structure
   %
   % :returns: - :matlabbatch: (structure)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   printBatchName('Lesion abnormalities');
 
diff --git a/src/batches/setBatchLesionOverlapMap.m b/src/batches/setBatchLesionOverlapMap.m
index 01c7af5e..3f7dfc37 100755
--- a/src/batches/setBatchLesionOverlapMap.m
+++ b/src/batches/setBatchLesionOverlapMap.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchLesionOverlapMap(matlabbatch, BIDS, opt, subLabel)
   %
   % Creates a batch for the lesion overlap map
@@ -12,6 +10,8 @@
   % :type matlabbatch: structure
   %
   % :returns: - :matlabbatch: (structure)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   printBatchName('Lesion overlap map');
 
diff --git a/src/batches/setBatchLesionSegmentation.m b/src/batches/setBatchLesionSegmentation.m
index 8a0a7e22..858cea1d 100755
--- a/src/batches/setBatchLesionSegmentation.m
+++ b/src/batches/setBatchLesionSegmentation.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchLesionSegmentation(matlabbatch, BIDS, opt, subLabel)
   %
   % Creates a batch to segment the anatomical image for lesion detection
@@ -12,6 +10,8 @@
   % :type matlabbatch: structure
   %
   % :returns: - :matlabbatch: (structure)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   printBatchName('Lesion segmentation');
 
diff --git a/src/batches/setBatchMeanAnatAndMask.m b/src/batches/setBatchMeanAnatAndMask.m
index 41839db5..cb661973 100644
--- a/src/batches/setBatchMeanAnatAndMask.m
+++ b/src/batches/setBatchMeanAnatAndMask.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchMeanAnatAndMask(matlabbatch, opt, funcFWHM, outputDir)
   %
   % Creates batxh to create mean anatomical image and a group mask
@@ -18,6 +16,7 @@
   %
   % :returns: - :matlabbatch: (structure)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   [BIDS, opt] = getData(opt);
 
diff --git a/src/batches/setBatchNormalizationSpatialPrepro.m b/src/batches/setBatchNormalizationSpatialPrepro.m
index effe07e1..918ae121 100644
--- a/src/batches/setBatchNormalizationSpatialPrepro.m
+++ b/src/batches/setBatchNormalizationSpatialPrepro.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchNormalizationSpatialPrepro(matlabbatch, opt, voxDim)
   %
   % Short description of what the function does goes here.
@@ -17,6 +15,7 @@
   %
   % :returns: - :matlabbatch: (structure)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   jobsToAdd = numel(matlabbatch) + 1;
 
diff --git a/src/batches/setBatchNormalize.m b/src/batches/setBatchNormalize.m
index 4416d37d..5af36e79 100644
--- a/src/batches/setBatchNormalize.m
+++ b/src/batches/setBatchNormalize.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchNormalize(matlabbatch, deformField, voxDim, imgToResample)
   %
   % Short description of what the function does goes here.
@@ -19,6 +17,7 @@
   %
   % :returns: - :matlabbatch: (structure)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   if nargin > 1 && ~isempty(deformField)
     matlabbatch{end + 1}.spm.spatial.normalise.write.subj.def(1) = deformField;
diff --git a/src/batches/setBatchPrintFigure.m b/src/batches/setBatchPrintFigure.m
index fbdac056..2f6fb363 100644
--- a/src/batches/setBatchPrintFigure.m
+++ b/src/batches/setBatchPrintFigure.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchPrintFigure(matlabbatch, figureName)
   %
   % template to creae new setBatch functions
@@ -14,6 +12,8 @@
   % :type figureName:  string
   %
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if spm('CmdLine', true)
 
diff --git a/src/batches/setBatchRealign.m b/src/batches/setBatchRealign.m
index a911aa12..f04d6e63 100644
--- a/src/batches/setBatchRealign.m
+++ b/src/batches/setBatchRealign.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [matlabbatch, voxDim] = setBatchRealign(varargin)
   %
   % Set the batch for realign / realign and reslice / realign and unwarp
@@ -25,9 +23,12 @@
   %
   % :returns: - :matlabbatch: (structure) (dimension)
   %           - :voxDim: (array) (dimension)
-
-  % TODO:
-  % make which image is resliced more consistent 'which = []'
+  %
+  % TODO::
+  %
+  %   make which image is resliced more consistent 'which = []'
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if numel(varargin) < 5
     [matlabbatch, BIDS, opt, subLabel] = deal(varargin{:});
diff --git a/src/batches/setBatchReslice.m b/src/batches/setBatchReslice.m
index 97a08d94..534a4f92 100644
--- a/src/batches/setBatchReslice.m
+++ b/src/batches/setBatchReslice.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchReslice(matlabbatch, referenceImg, sourceImages, interp)
   %
   % Set the batch for reslicing source images to the reference image resolution
@@ -18,6 +16,7 @@
   %
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('reslicing');
 
diff --git a/src/batches/setBatchResults.m b/src/batches/setBatchResults.m
index 84b73eab..4e4cf24b 100644
--- a/src/batches/setBatchResults.m
+++ b/src/batches/setBatchResults.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchResults(matlabbatch, result)
   %
   % Outputs the typical matlabbatch to compute the results for a given contrast
@@ -21,6 +19,8 @@
   % :returns: - :matlabbatch: (structure)
   %
   %
+  % (C) Copyright 2019 CPP_SPM developers
+
   result.outputNameStructure.sub = result.label;
   result.outputNameStructure.desc = result.Contrasts.Name;
   result.outputNameStructure.p = num2str(result.Contrasts.p);
diff --git a/src/batches/setBatchSTC.m b/src/batches/setBatchSTC.m
index 0d4d9658..462493a0 100644
--- a/src/batches/setBatchSTC.m
+++ b/src/batches/setBatchSTC.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSTC(matlabbatch, BIDS, opt, subLabel)
   %
   % Creates batch for slice timing correction
@@ -30,6 +28,7 @@
   % If not specified this function will take the mid-volume time point as reference
   % to do the slice timing correction
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   % get slice order
   sliceOrder = getSliceOrder(opt, 1);
diff --git a/src/batches/setBatchSaveCoregistrationMatrix.m b/src/batches/setBatchSaveCoregistrationMatrix.m
index ab9fb872..2af36499 100644
--- a/src/batches/setBatchSaveCoregistrationMatrix.m
+++ b/src/batches/setBatchSaveCoregistrationMatrix.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSaveCoregistrationMatrix(matlabbatch, BIDS, opt, subLabel)
   %
   % Short description of what the function does goes here.
@@ -19,6 +17,7 @@
   %
   % :returns: - :matlabbatch:
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('saving coregistration matrix');
 
diff --git a/src/batches/setBatchSegmentation.m b/src/batches/setBatchSegmentation.m
index 395cc588..2b86fe4b 100644
--- a/src/batches/setBatchSegmentation.m
+++ b/src/batches/setBatchSegmentation.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSegmentation(matlabbatch, opt, imageToSegment)
   %
   % Creates a batch to segment the anatomical image
@@ -16,6 +14,7 @@
   %
   % :returns: :matlabbatch: (structure)
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('Segmentation anatomical image');
 
diff --git a/src/batches/setBatchSelectAnat.m b/src/batches/setBatchSelectAnat.m
index e8e11bd1..b934ce5f 100644
--- a/src/batches/setBatchSelectAnat.m
+++ b/src/batches/setBatchSelectAnat.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSelectAnat(matlabbatch, BIDS, opt, subLabel)
   %
   % Creates a batch to set an anatomical image
@@ -26,6 +24,8 @@
   % - session to select the anat from = opt.anatReference.session (default = 1)
   %
   % We assume that the first anat of that type is the "correct" one
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('selecting anatomical image');
 
diff --git a/src/batches/setBatchSkullStripping.m b/src/batches/setBatchSkullStripping.m
index 52166108..db416ea3 100644
--- a/src/batches/setBatchSkullStripping.m
+++ b/src/batches/setBatchSkullStripping.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSkullStripping(matlabbatch, BIDS, opt, subLabel)
   %
   % Creates a batch to compute a brain mask based on the tissue probability maps
@@ -33,6 +31,8 @@
   % Any voxel with p(grayMatter) +  p(whiteMatter) + p(CSF) > threshold
   % will be included in the skull stripping mask.
   %
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('skull stripping');
 
diff --git a/src/batches/setBatchSmoothConImages.m b/src/batches/setBatchSmoothConImages.m
index 9e8d6dd0..f92b5a06 100644
--- a/src/batches/setBatchSmoothConImages.m
+++ b/src/batches/setBatchSmoothConImages.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSmoothConImages(matlabbatch, opt, funcFWHM, conFWHM)
   %
   % Creates a batch to smooth all the con images of all subjects
@@ -21,6 +19,7 @@
   %
   % :returns: - :matlabbatch:
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   printBatchName('smoothing contrast images');
 
diff --git a/src/batches/setBatchSmoothing.m b/src/batches/setBatchSmoothing.m
index f0e353de..349077bc 100644
--- a/src/batches/setBatchSmoothing.m
+++ b/src/batches/setBatchSmoothing.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSmoothing(matlabbatch, images, FWHM, prefix)
   %
   % Small wrapper to create smoothing batch
@@ -20,6 +18,7 @@
   % :returns: - :matlabbatch: (structure)
   %
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   printBatchName('smoothing images');
 
diff --git a/src/batches/setBatchSmoothingFunc.m b/src/batches/setBatchSmoothingFunc.m
index 3baf0487..e2aea02c 100644
--- a/src/batches/setBatchSmoothingFunc.m
+++ b/src/batches/setBatchSmoothingFunc.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSmoothingFunc(matlabbatch, BIDS, opt, subID, funcFWHM)
   %
   % Short description of what the function does goes here.
@@ -22,6 +20,7 @@
   % :returns: - :matlabbatch: (structure)
   %
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   printBatchName('smoothing functional images');
 
diff --git a/src/batches/setBatchSubjectLevelContrasts.m b/src/batches/setBatchSubjectLevelContrasts.m
index 593d4973..7791b17c 100644
--- a/src/batches/setBatchSubjectLevelContrasts.m
+++ b/src/batches/setBatchSubjectLevelContrasts.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSubjectLevelContrasts(matlabbatch, opt, subLabel, funcFWHM)
   %
   % Short description of what the function does goes here.
@@ -19,6 +17,7 @@
   %
   % :returns: - :matlabbatch:
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   printBatchName('subject level contrasts specification');
 
diff --git a/src/batches/setBatchSubjectLevelGLMSpec.m b/src/batches/setBatchSubjectLevelGLMSpec.m
index 65688901..70fd2795 100644
--- a/src/batches/setBatchSubjectLevelGLMSpec.m
+++ b/src/batches/setBatchSubjectLevelGLMSpec.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSubjectLevelGLMSpec(varargin)
   %
   % Short description of what the function does goes here.
@@ -18,6 +16,7 @@
   % :returns: - :argout1: (type) (dimension)
   %           - :argout2: (type) (dimension)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   [matlabbatch, BIDS, opt, subLabel, funcFWHM] =  deal(varargin{:});
 
diff --git a/src/batches/setBatchSubjectLevelResults.m b/src/batches/setBatchSubjectLevelResults.m
index ff2638d3..7a73cd55 100644
--- a/src/batches/setBatchSubjectLevelResults.m
+++ b/src/batches/setBatchSubjectLevelResults.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchSubjectLevelResults(varargin)
   %
   % Short description of what the function does goes here.
@@ -23,6 +21,7 @@
   %
   % :returns: - :matlabbatch: (structure)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   [matlabbatch, opt, subLabel, funcFWHM, iStep, iCon] = deal(varargin{:});
 
diff --git a/src/defaults/checkOptions.m b/src/defaults/checkOptions.m
index e5bb94e1..878184df 100644
--- a/src/defaults/checkOptions.m
+++ b/src/defaults/checkOptions.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function opt = checkOptions(opt)
   %
   % Check the option inputs and add any missing field with some defaults
@@ -19,10 +17,12 @@
   % - :opt: the option structure with missing values filled in by the defaults.
   %
   % REQUIRED FIELDS:
+  %
   %   - ``opt.taskName``
   %   - ``opt.dataDir``
   %
   % IMPORTANT OPTIONS (with their defaults):
+  %
   %   - ``opt.groups = {''}`` - group of subjects to analyze
   %   - ``opt.subjects = {[]}`` - suject to run in each group
   %     space where we conduct the analysis
@@ -37,6 +37,7 @@
   %     model to speficy and the contrasts to compute.
   %
   % OTHER OPTIONS (with their defaults):
+  %
   %     - ``opt.zeropad = 2`` - number of zeros used for padding subject numbers, in case
   %         subjects should be fetched by their number ``1`` and not their label ``O1'``.
   %     - ``opt.query`` - a structure used to specify other options to only run analysis on
@@ -51,17 +52,21 @@
   %         at normalization.
   %     - ``opt.STC_referenceSlice = []`` - reference slice for the slice timing correction.
   %         If left emtpy the mid-volume acquisition time point will be selected at run time.
-  %     - ``opt.sliceOrder = []`` - To be used if SPM can't extract slice info. NOT RECOMMENDED:
+  %     - ``opt.sliceOrder = []`` - To be used if SPM can't extract slice info. NOT RECOMMENDED,
   %         if you know the order in which slices were acquired, you should be able to recompute
   %         slice timing and add it to the json files in your BIDS data set.
-  %   -  ``opt.glmQA.do = true;`` - If set to ``true```the residual images of a
+  %     -  ``opt.glm.roibased.do``
+  %     -  ``opt.glm.QA.do = true`` - If set to ``true`` the residual images of a
   %         GLM at the subject levels will be used to estimate if there is any remaining structure
   %         in the GLM residuals (the power spectra are not flat) that could indicate
   %         the subject level results are likely confounded (see
-  %         ``plot_power_spectra_of_GLM_residuals``) and 'Accurate autocorrelation modeling
-  %         substantially improves fMRI reliability'
-  %         _https://www.nature.com/articles/s41467-019-09230-w.pdf
+  %         ``plot_power_spectra_of_GLM_residuals`` and `Accurate autocorrelation modeling
+  %         substantially improves fMRI reliability
+  %         <https://www.nature.com/articles/s41467-019-09230-w.pdf>`_ for more info.
+  %
+  %
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   fieldsToSet = setDefaultOption();
 
diff --git a/src/defaults/createDefaultModel.m b/src/defaults/createDefaultModel.m
index 0de2252f..9a541612 100644
--- a/src/defaults/createDefaultModel.m
+++ b/src/defaults/createDefaultModel.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function opt = createDefaultModel(BIDS, opt)
   %
   % Creates a default model json file.
@@ -49,6 +47,7 @@
   %
   %   createDefaultModel(BIDS, opt);
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   % TODO deal with the Transformations and Convolve fields
 
diff --git a/src/defaults/datasetDescriptionDefaults.m b/src/defaults/datasetDescriptionDefaults.m
index a9bc50bf..86d51462 100644
--- a/src/defaults/datasetDescriptionDefaults.m
+++ b/src/defaults/datasetDescriptionDefaults.m
@@ -1,6 +1,7 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function datasetDescription = datasetDescriptionDefaults()
+  %
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   datasetDescription.Name = 'cpp_spm outputs';
   datasetDescription.BIDSVersion = '1.4.1';
diff --git a/src/defaults/miss_hit.cfg b/src/defaults/miss_hit.cfg
index 636a9186..a9f91c98 100644
--- a/src/defaults/miss_hit.cfg
+++ b/src/defaults/miss_hit.cfg
@@ -1,10 +1 @@
-# styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
-line_length: 100
 regex_function_name: "[a-z]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*" # almost anything goes in the root folder
-copyright_entity: "CPP BIDS SPM-pipeline developpers"
-
-# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
-metric "cnest": limit 4
-metric "file_length": limit 400
-metric "cyc": limit 12
-metric "parameters": limit 6
\ No newline at end of file
diff --git a/src/defaults/returnDefaultResultsStructure.m b/src/defaults/returnDefaultResultsStructure.m
index 96cbeb08..7d1eaa21 100644
--- a/src/defaults/returnDefaultResultsStructure.m
+++ b/src/defaults/returnDefaultResultsStructure.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function results  = returnDefaultResultsStructure()
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   Contrasts =  struct( ...
                       'Name', '', ...
diff --git a/src/defaults/returnEmptyModel.m b/src/defaults/returnEmptyModel.m
index 3148a97f..d4664741 100644
--- a/src/defaults/returnEmptyModel.m
+++ b/src/defaults/returnEmptyModel.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function content = returnEmptyModel()
   %
   % Creates the content of a basic model.json file for GLM analysis with
@@ -22,6 +20,7 @@
   %   filename = fullfile(pwd, 'models', 'model-empty_smdl.json')
   %   spm_jsonwrite(filename, content, jsonOptions);
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   content.Name = ' ';
   content.Description = ' ';
diff --git a/src/defaults/spm_my_defaults.m b/src/defaults/spm_my_defaults.m
index 43b67496..eac7591e 100644
--- a/src/defaults/spm_my_defaults.m
+++ b/src/defaults/spm_my_defaults.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function spm_my_defaults()
   %
   % Short description of what the function does goes here.
@@ -15,6 +13,8 @@ function spm_my_defaults()
   % When "not enough" information is specified in the batch files, SPM falls
   % back on the defaults to fill in the blanks. This allows to make the
   % script simpler.
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   global defaults
 
diff --git a/src/fieldmaps/getBlipDirection.m b/src/fieldmaps/getBlipDirection.m
index 33bbb2db..1d8660db 100644
--- a/src/fieldmaps/getBlipDirection.m
+++ b/src/fieldmaps/getBlipDirection.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function blipDir = getBlipDirection(metadata)
   %
   % Gets the total read out time of a sequence.
@@ -15,6 +13,7 @@
   %
   % Used to create the voxel dsiplacement map (VDM) from the fieldmap
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   blipDir = 1;
 
diff --git a/src/fieldmaps/getMetadataFromIntendedForFunc.m b/src/fieldmaps/getMetadataFromIntendedForFunc.m
index 29d8ee57..1bfeb148 100644
--- a/src/fieldmaps/getMetadataFromIntendedForFunc.m
+++ b/src/fieldmaps/getMetadataFromIntendedForFunc.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [totalReadoutTime, blipDir] = getMetadataFromIntendedForFunc(BIDS, fmapMetadata)
   %
   % Gets metadata of the associated bold file:
@@ -26,6 +24,8 @@
   %
   %    - if there are several func file for this fmap and they have different
   %    characteristic this may require creating a VDM for each
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   for  iFile = 1:size(fmapMetadata.IntendedFor)
 
diff --git a/src/fieldmaps/getTotalReadoutTime.m b/src/fieldmaps/getTotalReadoutTime.m
index f9f2122a..46c5c5c1 100644
--- a/src/fieldmaps/getTotalReadoutTime.m
+++ b/src/fieldmaps/getTotalReadoutTime.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function totalReadoutTime = getTotalReadoutTime(metadata)
   %
   % Gets the total read out time of a sequence.
@@ -15,6 +13,7 @@
   %
   % Used to create the voxel dsiplacement map (VDM) from the fieldmap
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   totalReadoutTime = '';
 
diff --git a/src/fieldmaps/getVdmFile.m b/src/fieldmaps/getVdmFile.m
index 2c96416e..51bb36c0 100644
--- a/src/fieldmaps/getVdmFile.m
+++ b/src/fieldmaps/getVdmFile.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function vdmFile = getVdmFile(BIDS, opt, boldFilename)
   %
   % returns the voxel displacement map associated with a given bold file
@@ -17,6 +15,7 @@
   %
   % :returns: - :vdmFile: (string)
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   vdmFile = '';
 
diff --git a/src/getAnatFilename.m b/src/getAnatFilename.m
index 880f6838..f0b2dd37 100644
--- a/src/getAnatFilename.m
+++ b/src/getAnatFilename.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [anatImage, anatDataDir] = getAnatFilename(BIDS, subLabel, opt)
   %
   % Get the filename and the directory of an anat file for a given session and run.
@@ -21,6 +19,7 @@
   % :returns: - :anatImage: (string)
   %           - :anatDataDir: (string)
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   anatSuffix = opt.anatReference.type;
   anatSession = opt.anatReference.session;
diff --git a/src/getBoldFilename.m b/src/getBoldFilename.m
index 302856b4..243e6495 100644
--- a/src/getBoldFilename.m
+++ b/src/getBoldFilename.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [boldFileName, subFuncDataDir] = getBoldFilename(varargin)
   %
   % Get the filename and the directory of a bold file for a given session /
@@ -28,6 +26,7 @@
   %           - :subFuncDataDir: (string)
   %
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, subID, sessionID, runID, opt] = deal(varargin{:});
 
diff --git a/src/getData.m b/src/getData.m
index 7277c20f..fd60aec6 100644
--- a/src/getData.m
+++ b/src/getData.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [BIDS, opt] = getData(opt, BIDSdir, type)
   %
   % Reads the specified BIDS data set and updates the list of subjects to analyze.
@@ -27,6 +25,8 @@
   %  IMPORTANT NOTE: if you specify the type variable for T1w then you must
   %  make sure that the T1w.json is also present in the anat folder because
   %  of the way the bids.query function works at the moment
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 2 || (exist('BIDSdir', 'var') && isempty(BIDSdir))
     % The directory where the derivatives are located
diff --git a/src/getFuncVoxelDims.m b/src/getFuncVoxelDims.m
index 296398fc..bb38ab19 100644
--- a/src/getFuncVoxelDims.m
+++ b/src/getFuncVoxelDims.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [voxDim, opt] = getFuncVoxelDims(opt, subFuncDataDir, prefix, fileName)
   %
   % Short description of what the function does goes here.
@@ -22,6 +20,7 @@
   %
   %
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   % get native resolution to reuse it at normalisation;
   if ~isempty(opt.funcVoxelDims) % If voxel dimensions is defined in the opt
diff --git a/src/getInfo.m b/src/getInfo.m
index 0ea7af07..c2ca3aed 100644
--- a/src/getInfo.m
+++ b/src/getInfo.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function varargout = getInfo(BIDS, subLabel, opt, info, varargin)
   %
   % Wrapper function to fetch specific info in a BIDS structure returned by
@@ -9,7 +7,7 @@
   %
   %   varargout = getInfo(BIDS, subLabel, opt, info, varargin)
   %
-  % If info = ``sessions`, this returns name of the sessions and their number::
+  % If info = ``sessions``, this returns name of the sessions and their number::
   %
   %   [sessions, nbSessions] = getInfo(BIDS, subID, opt, 'sessions')
   %
@@ -47,6 +45,7 @@
   % :param type:            datatype (``bold``, ``events``, ``physio``)
   % :type type:             string
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   varargout = {}; %#ok<*NASGU>
 
diff --git a/src/getMeanFuncFilename.m b/src/getMeanFuncFilename.m
index b9057cc6..bea6ea44 100644
--- a/src/getMeanFuncFilename.m
+++ b/src/getMeanFuncFilename.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [meanImage, meanFuncDir] = getMeanFuncFilename(BIDS, subLabel, opt)
   %
   % Get the filename and the directory of an mean functional file.
@@ -18,6 +16,7 @@
   % :returns: - :meanImage: (string)
   %           - :meanFuncDir: (string)
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   sessions = getInfo(BIDS, subLabel, opt, 'Sessions');
   runs = getInfo(BIDS, subLabel, opt, 'Runs', sessions{1});
diff --git a/src/getPrefix.m b/src/getPrefix.m
index 5c8c334b..ef334d9b 100644
--- a/src/getPrefix.m
+++ b/src/getPrefix.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [prefix, motionRegressorPrefix] = getPrefix(step, opt, funcFWHM)
   %
   % Generates prefix to append to file name to look for
@@ -19,6 +17,7 @@
   %           - :motionRegressorPrefix:
   %
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 3
     funcFWHM = 0;
diff --git a/src/getRealignParamFile.m b/src/getRealignParamFile.m
index d5cc6111..e049ce9b 100644
--- a/src/getRealignParamFile.m
+++ b/src/getRealignParamFile.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function realignParamFile = getRealignParamFile(fullpathBoldFileName, prefix)
   %
   % Short description of what the function does goes here.
@@ -18,6 +16,8 @@
   %
   % :returns: - :argout1: (type) (dimension)
   %           - :argout2: (type) (dimension)
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [funcDataDir, boldFileName] = spm_fileparts(fullpathBoldFileName);
 
diff --git a/src/getSliceOrder.m b/src/getSliceOrder.m
index 8cc2f553..1d2e1037 100644
--- a/src/getSliceOrder.m
+++ b/src/getSliceOrder.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function sliceOrder = getSliceOrder(opt, verbose)
   %
   % Get the slice order information from the BIDS metadata or from the ``opt``
@@ -25,6 +23,7 @@
   %
   % See also: ``bidsSTC``
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 2
     verbose = false;
diff --git a/src/group_level/getGrpLevelContrastToCompute.m b/src/group_level/getGrpLevelContrastToCompute.m
index 52ec91ad..d7bedf6d 100644
--- a/src/group_level/getGrpLevelContrastToCompute.m
+++ b/src/group_level/getGrpLevelContrastToCompute.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function [grpLvlCon, iStep] = getGrpLevelContrastToCompute(opt)
   %
   % Returns the autocontrast part of the dataset step of the BIDS model
@@ -14,6 +12,7 @@
   % :returns: - :grpLvlCon:
   %           - :iStep:
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   model = spm_jsonread(opt.model.file);
 
diff --git a/src/group_level/getRFXdir.m b/src/group_level/getRFXdir.m
index 7a96acba..a54e58b9 100644
--- a/src/group_level/getRFXdir.m
+++ b/src/group_level/getRFXdir.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function rfxDir = getRFXdir(opt, funcFWHM, conFWHM)
   %
   % Sets the name the group level analysis directory and creates it if it does not exist
@@ -21,6 +19,7 @@
   %
   % :returns: :rfxDir: (string) Fullpath of the group level directory
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   glmDirName = createGlmDirName(opt, funcFWHM);
 
diff --git a/src/reports/copyFigures.m b/src/reports/copyFigures.m
index 04bcce9f..6a939581 100644
--- a/src/reports/copyFigures.m
+++ b/src/reports/copyFigures.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function copyFigures(BIDS, opt, subLabel)
   %
   % Copy the figures from spatial preprocessing into a separate folder.
@@ -16,6 +14,7 @@ function copyFigures(BIDS, opt, subLabel)
   % :type subLabel: string
   %
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   imgNb = copyGraphWindownOutput(opt, subLabel, 'realign');
 
diff --git a/src/reports/copyGraphWindownOutput.m b/src/reports/copyGraphWindownOutput.m
index a7821cd0..825043db 100644
--- a/src/reports/copyGraphWindownOutput.m
+++ b/src/reports/copyGraphWindownOutput.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function imgNb = copyGraphWindownOutput(opt, subID, action, imgNb)
   %
   % Looks into the current directory for an ``spm_.*imgNb.png`` file and moves it into
@@ -23,6 +21,7 @@
   %
   % :returns: :imgNb: (integer) number of the next image to get.
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   if nargin < 4 || isempty(imgNb)
     imgNb = 1;
diff --git a/src/reports/reportBIDS.m b/src/reports/reportBIDS.m
index 4c617840..e0943d19 100644
--- a/src/reports/reportBIDS.m
+++ b/src/reports/reportBIDS.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function reportBIDS(opt)
   %
   % Prints out a human readable description of a BIDS data set.
@@ -16,6 +14,8 @@ function reportBIDS(opt)
   %
   %     - save output in the derivatires folder
   %       derivativeDir = fullfile(rawDir, '..', 'derivatives', 'cpp_spm');
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   bids.report(opt.dataDir);
 
diff --git a/src/results/returnName.m b/src/results/returnName.m
index 8fcc2ffb..12fb43d1 100644
--- a/src/results/returnName.m
+++ b/src/results/returnName.m
@@ -1,6 +1,8 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function name = returnName(result)
+  %
+  % To help naming of files generated when computing results of a given contrast
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   name = sprintf('%s_p-%0.3f_k-%i_MC-%s', ...
                  result.Contrasts.Name, ...
diff --git a/src/results/setMontage.m b/src/results/setMontage.m
index 23e949d1..0507d67f 100644
--- a/src/results/setMontage.m
+++ b/src/results/setMontage.m
@@ -1,11 +1,11 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function montage = setMontage(result)
-
+  %
   % TO DO
   % - adapt so that the background image is in MNI only if opt.space is MNI
   % - add possibility to easily select mean functional or the anatomical:
   %   - at the group level or subject level
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   montage.background = {result.Output.montage.background};
   montage.orientation = result.Output.montage.orientation;
diff --git a/src/setDerivativesDir.m b/src/setDerivativesDir.m
index b0cf3183..7b27b581 100644
--- a/src/setDerivativesDir.m
+++ b/src/setDerivativesDir.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function opt = setDerivativesDir(opt)
   %
   % Sets the derivatives folder and the directory where to save the SPM jobs.
@@ -17,34 +15,36 @@
   %   - :opt: structure or json filename containing the options. See
   %           ``checkOptions()`` and ``loadAndCheckOptions()``.
   %
-  % Examples:
-  %   % opt.dataDir = '/home/remi/data';
-  %   % opt.taskName = 'testTask';
-  %   % opt = setDerivativesDir(opt);
-  %   %
-  %   % disp(opt.derivativesDir)
-  %   %|| '/home/remi/data/../derivatives/cpp_spm'
-  %   %
-  %   % disp(opt.opt.jobsDir)
-  %   %|| '/home/remi/data/../derivatives/cpp_spm/JOBS/testTask
+  % Examples::
+  %
+  %   opt.dataDir = '/home/remi/data';
+  %   opt.taskName = 'testTask';
+  %   opt = setDerivativesDir(opt);
+  %
+  %   disp(opt.derivativesDir)
+  %   '/home/remi/data/../derivatives/cpp_spm'
+  %
+  %   disp(opt.opt.jobsDir)
+  %   '/home/remi/data/../derivatives/cpp_spm/JOBS/testTask
+  %
+  %   opt.dataDir = '/home/remi/data';
+  %   opt.dataDir = '/home/remi/otherFolder';
+  %   opt.taskName = 'testTask';
+  %   opt = setDerivativesDir(opt);
+  %
+  %   disp(opt.derivativesDir)
+  %   '/home/remi/otherFolder/derivatives/cpp_spm'
   %
-  %   % opt.dataDir = '/home/remi/data';
-  %   % opt.dataDir = '/home/remi/otherFolder';
-  %   % opt.taskName = 'testTask';
-  %   % opt = setDerivativesDir(opt);
-  %   %
-  %   % disp(opt.derivativesDir)
-  %   %|| '/home/remi/otherFolder/derivatives/cpp_spm'
+  %   opt.dataDir = '/home/remi/data';
+  %   opt.dataDir = '/home/remi/derivatives/preprocessing';
+  %   opt.taskName = 'testTask';
+  %   opt = setDerivativesDir(opt);
   %
-  %   % opt.dataDir = '/home/remi/data';
-  %   % opt.dataDir = '/home/remi/derivatives/preprocessing';
-  %   % opt.taskName = 'testTask';
-  %   % opt = setDerivativesDir(opt);
-  %   %
-  %   % disp(opt.derivativesDir)
-  %   %|| '/home/remi/otherFolder/derivatives/preprocessing'
+  %   disp(opt.derivativesDir)
+  %   '/home/remi/otherFolder/derivatives/preprocessing'
   %
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if ~isfield(opt, 'derivativesDir') || isempty(opt.derivativesDir)
     opt.derivativesDir = fullfile(opt.dataDir, '..', 'derivatives', 'cpp_spm');
diff --git a/src/setStatsDir.m b/src/setStatsDir.m
index 48aa4072..637f1420 100644
--- a/src/setStatsDir.m
+++ b/src/setStatsDir.m
@@ -1,6 +1,10 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function opt = setStatsDir(opt)
+  %
+  % USAGE::
+  %
+  %  opt = setStatsDir(opt)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   opt = setDerivativesDir(opt);
 
diff --git a/src/subject_level/convertOnsetTsvToMat.m b/src/subject_level/convertOnsetTsvToMat.m
index c561f122..3076428e 100644
--- a/src/subject_level/convertOnsetTsvToMat.m
+++ b/src/subject_level/convertOnsetTsvToMat.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function fullpathOnsetFileName = convertOnsetTsvToMat(opt, tsvFile)
   %
   % Converts an  events.tsv file to an onset file suitable for SPM subject level
@@ -16,8 +14,9 @@
   % :param tsvFile:
   % :type tsvFile: string
   %
-  % :returns: - :fullpathOnsetFileName: (string) name of the output `.mat` file.
+  % :returns: :fullpathOnsetFileName: (string) name of the output ``.mat`` file.
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   %
   [pth, file, ext] = spm_fileparts(tsvFile);
diff --git a/src/subject_level/createAndReturnOnsetFile.m b/src/subject_level/createAndReturnOnsetFile.m
index 73e50eed..92a22ad6 100644
--- a/src/subject_level/createAndReturnOnsetFile.m
+++ b/src/subject_level/createAndReturnOnsetFile.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function onsetFileName = createAndReturnOnsetFile(opt, subID, tsvFile, funcFWHM)
   %
   % For a given events.tsv file it creates a .mat file that can directly be used
@@ -20,9 +18,10 @@
   %                  GLM. Necessary for the GLM directory.
   % :type funcFWHM: float
   %
-  % :returns: - :onsetFileName: (string) fullpath name of the file created.
-  %                             Removes any prefix.
+  % :returns: :onsetFileName: (string) fullpath name of the file created.
+  %
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   onsetFileName = convertOnsetTsvToMat(opt, tsvFile);
 
diff --git a/src/subject_level/deleteResidualImages.m b/src/subject_level/deleteResidualImages.m
index a6b10bf4..59838998 100644
--- a/src/subject_level/deleteResidualImages.m
+++ b/src/subject_level/deleteResidualImages.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function deleteResidualImages(ffxDir)
   %
   % USAGE::
@@ -9,6 +7,7 @@ function deleteResidualImages(ffxDir)
   % :param ffxDir:
   % :type ffxDir: string
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   delete(fullfile(ffxDir, 'Res_*.nii'));
   delete(fullfile(ffxDir, 'res4d.nii*'));
diff --git a/src/subject_level/getBoldFilenameForFFX.m b/src/subject_level/getBoldFilenameForFFX.m
index 117ed609..b53b6f3e 100644
--- a/src/subject_level/getBoldFilenameForFFX.m
+++ b/src/subject_level/getBoldFilenameForFFX.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [boldFileName, prefix] = getBoldFilenameForFFX(varargin)
   %
   % Gets the filename for this bold run for this task for the FFX setup
@@ -26,6 +24,7 @@
   %           - :prefix: (srting)
   %
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, opt, subID, funcFWHM, iSes, iRun] =  deal(varargin{:});
 
diff --git a/src/subject_level/getFFXdir.m b/src/subject_level/getFFXdir.m
index cad5cb71..677ec0cd 100644
--- a/src/subject_level/getFFXdir.m
+++ b/src/subject_level/getFFXdir.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function ffxDir = getFFXdir(subLabel, funcFWFM, opt)
   %
   % Sets the name the FFX directory and creates it if it does not exist
@@ -17,6 +15,7 @@
   %
   % :returns: - :ffxDir: (string)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   glmDirName = createGlmDirName(opt, funcFWFM);
 
diff --git a/src/subject_level/specifyContrasts.m b/src/subject_level/specifyContrasts.m
index 811c6e27..7b2e5854 100644
--- a/src/subject_level/specifyContrasts.m
+++ b/src/subject_level/specifyContrasts.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function contrasts = specifyContrasts(ffxDir, taskName, opt)
   %
   % Specifies the first level contrasts
@@ -30,6 +28,8 @@
   %     Sn(1) R4
   %     Sn(1) R5
   %     Sn(1) R6
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   load(fullfile(ffxDir, 'SPM.mat'));
 
diff --git a/src/templates/bidsTemplateWorkflow.m b/src/templates/bidsTemplateWorkflow.m
index 39721e4c..2294c51b 100644
--- a/src/templates/bidsTemplateWorkflow.m
+++ b/src/templates/bidsTemplateWorkflow.m
@@ -1,8 +1,7 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function bidsTemplateWorkflow(opt)
   %
   %
+  % (C) Copyright 2021 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'workflow name');
 
diff --git a/src/templates/setBatchTemplate.m b/src/templates/setBatchTemplate.m
index 7a7536b6..f17b0d03 100644
--- a/src/templates/setBatchTemplate.m
+++ b/src/templates/setBatchTemplate.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function matlabbatch = setBatchTemplate(matlabbatch, BIDS, opt, subID, info, varargin)
   %
   % template to creae new setBatch functions
@@ -12,6 +10,8 @@
   % :type matlabbatch:
   %
   % :returns: - :matlabbatch: (structure) The matlabbatch ready to run the spm job
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   printBatchName('name for this batch');
 
diff --git a/src/templates/templateFunction.m b/src/templates/templateFunction.m
index 6897f2f2..c80726d3 100644
--- a/src/templates/templateFunction.m
+++ b/src/templates/templateFunction.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [argout1, argout2] = templateFunction(argin1, argin2, argin3)
   %
   % Short description of what the function does goes here.
@@ -23,6 +21,8 @@
   %
   %    - item 1
   %    - item 2
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   % The code goes below
 
diff --git a/src/templates/templateFunctionExample.m b/src/templates/templateFunctionExample.m
index 941690b5..d0bd6970 100644
--- a/src/templates/templateFunctionExample.m
+++ b/src/templates/templateFunctionExample.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function templateFunctionExample()
   % This function illustrates a documentation test defined for MOdox.
   % Other than that it does absolutely nothinghort description of what
@@ -36,6 +34,8 @@ function templateFunctionExample()
   %
   %
   % % tests end here because test indentation has ended
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   % The code goes below
 
diff --git a/src/templates/templateGetOption.m b/src/templates/templateGetOption.m
index 4946a976..797a3540 100644
--- a/src/templates/templateGetOption.m
+++ b/src/templates/templateGetOption.m
@@ -1,8 +1,9 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function opt = templateGetOption()
+  %
   % returns a structure that contains the options chosen by the user to return
   % the different workflows
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 1
     opt = [];
diff --git a/src/unzipImgAndReturnsFullpathName.m b/src/unzipImgAndReturnsFullpathName.m
index b8a4d6eb..0f4681c8 100644
--- a/src/unzipImgAndReturnsFullpathName.m
+++ b/src/unzipImgAndReturnsFullpathName.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function unzippedFullpathImgName = unzipImgAndReturnsFullpathName(fullpathImgName)
   %
   % Unzips an image if necessary
@@ -18,6 +16,7 @@
   %   - make it work on several images
   %
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [directory, filename, ext] = spm_fileparts(fullpathImgName);
 
diff --git a/src/utils/checkDependencies.m b/src/utils/checkDependencies.m
index 2dd645ce..dfb09d5b 100644
--- a/src/utils/checkDependencies.m
+++ b/src/utils/checkDependencies.m
@@ -1,20 +1,14 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function checkDependencies()
   %
-  % Checks that that the right dependencies are installed:
-  % - SPM
-  % - Nifti tools
-  % Also loads the spm defaults.
+  % Checks that that the right dependencies are installeda and
+  % loads the spm defaults.
   %
   % USAGE::
   %
   %   checkDependencies()
   %
-  % .. TODO:
-  %    - refactor in a several sub functions to cehck each dependency
-  %    - need to check other dependencies (bids-matlab, spmup)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   fprintf('Checking dependencies\n');
 
diff --git a/src/utils/cleanCrash.m b/src/utils/cleanCrash.m
index c8cce61d..ebc44640 100644
--- a/src/utils/cleanCrash.m
+++ b/src/utils/cleanCrash.m
@@ -1,15 +1,14 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function cleanCrash()
   %
   % Removes any files left over from a previous unfinished run of the pipeline,
-  % like any *.png imgages
+  % like any ``*.png`` imgages
   %
   % USAGE::
   %
   %   cleanCrash()
   %
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   files = {'spm.*.png'};
 
diff --git a/src/utils/createDataDictionary.m b/src/utils/createDataDictionary.m
index 973b1c0d..f7073d11 100644
--- a/src/utils/createDataDictionary.m
+++ b/src/utils/createDataDictionary.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function createDataDictionary(subFuncDataDir, fileName, nbColums)
   %
   % Short description of what the function does goes here.
@@ -15,6 +13,7 @@ function createDataDictionary(subFuncDataDir, fileName, nbColums)
   % :param nbColums: Number of extra columns to add as censoring regressors.
   % :type nbColums: integer
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   namecColumns = { ...
                   'trans_x', ...
diff --git a/src/utils/createDerivativeDir.m b/src/utils/createDerivativeDir.m
index dd947ac0..2f4b7fef 100644
--- a/src/utils/createDerivativeDir.m
+++ b/src/utils/createDerivativeDir.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function  createDerivativeDir(opt)
   %
   % Creates the derivative folder if it does not exist.
@@ -11,6 +9,7 @@ function  createDerivativeDir(opt)
   % :param opt: Options chosen for the analysis. See ``checkOptions()``.
   % :type opt: structure
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   if ~exist(opt.derivativesDir, 'dir')
     mkdir(opt.derivativesDir);
diff --git a/src/utils/createGlmDirName.m b/src/utils/createGlmDirName.m
index 8406337f..43e5dcd9 100644
--- a/src/utils/createGlmDirName.m
+++ b/src/utils/createGlmDirName.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function glmDirName = createGlmDirName(opt, FWHM)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   glmDirName = ['task-', opt.taskName, ...
                 '_space-' opt.space, ...
diff --git a/src/utils/getEnvInfo.m b/src/utils/getEnvInfo.m
index 6d54cf54..0f8734ba 100644
--- a/src/utils/getEnvInfo.m
+++ b/src/utils/getEnvInfo.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function [OS, GeneratedBy] = getEnvInfo()
   %
   % Gets information about the environement and operating system to help generate
@@ -12,6 +10,7 @@
   % :returns: :OS: (structure) (dimension)
   %           :GeneratedBy: (structure) (dimension)
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   GeneratedBy(1).name = 'cpp_spm';
   GeneratedBy(1).Version =  getVersion();
diff --git a/src/utils/getSubjectList.m b/src/utils/getSubjectList.m
index 75d05ef1..9bb2a3ae 100644
--- a/src/utils/getSubjectList.m
+++ b/src/utils/getSubjectList.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function opt = getSubjectList(BIDS, opt)
   %
   % Returns the subjects to analyze in ``opt.subjects``
@@ -38,6 +36,8 @@
   %
   %     opt.groups = {''};
   %     opt.subjects = {'01', 'cont01', 'cat02', 'ctrl02', 'blind01'};
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   allSubjects = bids.query(BIDS, 'subjects');
 
diff --git a/src/utils/getVersion.m b/src/utils/getVersion.m
index a0ef2b7a..f3471a6a 100644
--- a/src/utils/getVersion.m
+++ b/src/utils/getVersion.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function versionNumber = getVersion()
   %
   % Reads the version number of the pipeline from the txt file in the root of the
@@ -11,6 +9,7 @@
   %
   % :returns: :versionNumber: (string) Use semantic versioning format (like v0.1.0)
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   try
     versionNumber = fileread(fullfile(fileparts(mfilename('fullpath')), ...
diff --git a/src/utils/isOctave.m b/src/utils/isOctave.m
index 5fe03b9f..a0c14fa7 100644
--- a/src/utils/isOctave.m
+++ b/src/utils/isOctave.m
@@ -1,6 +1,3 @@
-% (C) Copyright 2020 Agah Karakuzu
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function retval = isOctave()
   %
   % Returns true if the environment is Octave.
@@ -11,6 +8,8 @@
   %
   % :returns: :retval: (boolean)
   %
+  % (C) Copyright 2020 Agah Karakuzu
+  % (C) Copyright 2020 CPP_SPM developers
 
   persistent cacheval   % speeds up repeated calls
 
diff --git a/src/utils/loadAndCheckOptions.m b/src/utils/loadAndCheckOptions.m
index 72df76b5..5ee90829 100644
--- a/src/utils/loadAndCheckOptions.m
+++ b/src/utils/loadAndCheckOptions.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function opt = loadAndCheckOptions(optionJsonFile)
   %
   % Loads the json file provided describing the options of an analysis. It then checks
@@ -23,6 +21,8 @@
   % .. TODO
   %
   %    - add test for when the input is a structure.
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 1 || isempty(optionJsonFile)
     optionJsonFile = spm_select('FPList', ...
diff --git a/src/utils/manageWorkersPool.m b/src/utils/manageWorkersPool.m
index b5a8c08b..76a1f3e6 100644
--- a/src/utils/manageWorkersPool.m
+++ b/src/utils/manageWorkersPool.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function manageWorkersPool(action, opt)
   %
   % Check matlab version and opens pool of workers for parallel work.
@@ -19,6 +17,7 @@ function manageWorkersPool(action, opt)
   %    opt.parallelize.nbWorkers = 3;
   %    opt.parallelize.killOnExit = true;
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if ~opt.parallelize.do
     opt.parallelize.nbWorkers = 1;
diff --git a/src/utils/printBatchName.m b/src/utils/printBatchName.m
index 32471cfe..8d103b6d 100644
--- a/src/utils/printBatchName.m
+++ b/src/utils/printBatchName.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function printBatchName(batchName)
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   fprintf(1, '\n BUILDING JOB: %s\n', lower(batchName));
 
diff --git a/src/utils/printCredits.m b/src/utils/printCredits.m
index 5e3cb4d7..d1122a28 100644
--- a/src/utils/printCredits.m
+++ b/src/utils/printCredits.m
@@ -1,10 +1,11 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function printCredits()
+  %
+  % TODO: use the .zenodo.json to load contributors
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   versionNumber = getVersion();
 
-  % TODO: use the .zenodo.json to load contributors
   contributors = { ...
                   'Mohamed Rezk', ...
                   'Remi Gau', ...
diff --git a/src/utils/printProcessingRun.m b/src/utils/printProcessingRun.m
index 29769001..7ac315cb 100644
--- a/src/utils/printProcessingRun.m
+++ b/src/utils/printProcessingRun.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function printProcessingRun(groupName, iSub, subID, iSes, iRun)
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   fprintf(1, ...
           [ ...
diff --git a/src/utils/printProcessingSubject.m b/src/utils/printProcessingSubject.m
index a0668d42..d7131e87 100644
--- a/src/utils/printProcessingSubject.m
+++ b/src/utils/printProcessingSubject.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function printProcessingSubject(iSub, subLabel)
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   fprintf(1, [ ...
               ' PROCESSING SUBJECT No.: %i ' ...
diff --git a/src/utils/printWorklowName.m b/src/utils/printWorklowName.m
index 9b4155fd..395c08b8 100644
--- a/src/utils/printWorklowName.m
+++ b/src/utils/printWorklowName.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function printWorklowName(workflowName)
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   fprintf(1, '\n\n\nWORKFLOW: %s\n\n', upper(workflowName));
 
diff --git a/src/utils/removeSpmPrefix.m b/src/utils/removeSpmPrefix.m
index 0ea6e3c4..cb5a2ba2 100644
--- a/src/utils/removeSpmPrefix.m
+++ b/src/utils/removeSpmPrefix.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function image = removeSpmPrefix(image, prefix)
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   basename = spm_file(image, 'basename');
   tmp = spm_file(image, 'basename', basename(length(prefix) + 1:end));
diff --git a/src/utils/rmTrialTypeStr.m b/src/utils/rmTrialTypeStr.m
index 82116dd6..cc5063c5 100644
--- a/src/utils/rmTrialTypeStr.m
+++ b/src/utils/rmTrialTypeStr.m
@@ -1,5 +1,6 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
 function conName = rmTrialTypeStr(conName)
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   conName = strrep(conName, 'trial_type.', '');
 
diff --git a/src/utils/saveMatlabBatch.m b/src/utils/saveMatlabBatch.m
index 7d6c7ff0..82212ff4 100644
--- a/src/utils/saveMatlabBatch.m
+++ b/src/utils/saveMatlabBatch.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function saveMatlabBatch(matlabbatch, batchType, opt, subID)
   %
   % Also save some basic environnment info.
@@ -18,6 +16,7 @@ function saveMatlabBatch(matlabbatch, batchType, opt, subID)
   % :type subID: string
   %
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   if nargin < 4 || isempty(subID)
     subID = 'group';
diff --git a/src/utils/saveOptions.m b/src/utils/saveOptions.m
index 0334f275..df3964c0 100644
--- a/src/utils/saveOptions.m
+++ b/src/utils/saveOptions.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function saveOptions(opt)
   %
   % Short description of what the function does goes here.
@@ -11,6 +9,7 @@ function saveOptions(opt)
   % :param opt: Options chosen for the analysis. See ``checkOptions()``.
   % :type opt: structure
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   optionDir = fullfile(pwd, 'cfg');
   [~, ~, ~] = mkdir(optionDir);
diff --git a/src/utils/setFields.m b/src/utils/setFields.m
index 907dcb7a..a82a0d87 100644
--- a/src/utils/setFields.m
+++ b/src/utils/setFields.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function structure = setFields(structure, fieldsToSet, overwrite)
   %
   % Recursively loop through the fields of a target ``structure`` and sets the values
@@ -22,6 +20,7 @@
   % :returns: - :structure: (structure)
   %
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if isempty(fieldsToSet)
     return
@@ -68,6 +67,8 @@
 
 function structure = setFieldToIfNotPresent(structure, fieldName, value)
   if ~isfield(structure, fieldName)
-    structure.(fieldName) = value;
+    for i = 1:numel(structure)
+      structure(i).(fieldName) = value;
+    end
   end
 end
diff --git a/src/utils/setGraphicWindow.m b/src/utils/setGraphicWindow.m
index 2d75a2c6..943cc27d 100644
--- a/src/utils/setGraphicWindow.m
+++ b/src/utils/setGraphicWindow.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function [interactiveWindow, graphWindow, cmdLine] = setGraphicWindow()
   %
   % Short description of what the function does goes here.
@@ -19,6 +17,7 @@
   % :returns: - :argout1: (type) (dimension)
   %           - :argout2: (type) (dimension)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   interactiveWindow = [];
   graphWindow = [];
diff --git a/src/utils/validationInputFile.m b/src/utils/validationInputFile.m
index 10cf7aec..23b7dbdd 100644
--- a/src/utils/validationInputFile.m
+++ b/src/utils/validationInputFile.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function files = validationInputFile(dir, fileNamePattern, prefix)
   %
   % Looks for file name pattern in a given directory and returns all the files
@@ -41,6 +39,7 @@
   % % tissueProbaMaps = validationInputFile(anatDataDir, anatImage, 'c[12]');
   %
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   % try to guess directory in case a fullpath filename was given
   if isempty(dir)
diff --git a/src/utils/writeDatasetDescription.m b/src/utils/writeDatasetDescription.m
index c7641e28..7699c682 100644
--- a/src/utils/writeDatasetDescription.m
+++ b/src/utils/writeDatasetDescription.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function writeDatasetDescription(opt)
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   oldDatasetDescription = spm_jsonread(fullfile(opt.derivativesDir, 'dataset_description.json'));
 
@@ -8,7 +8,7 @@ function writeDatasetDescription(opt)
 
   if isfield(oldDatasetDescription, 'DatasetDOI')
     newDatasetDescription.SourceDatasets{1}.DOI = ...
-        oldDatasetDescription.DatasetDOI;
+     oldDatasetDescription.DatasetDOI;
   end
 
   spm_jsonwrite( ...
diff --git a/src/workflows/bidsConcatBetaTmaps.m b/src/workflows/bidsConcatBetaTmaps.m
index dc757327..ed11cc87 100644
--- a/src/workflows/bidsConcatBetaTmaps.m
+++ b/src/workflows/bidsConcatBetaTmaps.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
   %
   % Make 4D images of beta and t-maps for the MVPA. ::
@@ -15,6 +13,7 @@ function bidsConcatBetaTmaps(opt, funcFWHM, deleteIndBeta, deleteIndTmaps)
   % :param deleteIndTmaps: decide to delete t-maps
   % :type funcFWHM: (boolean)
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   % delete individual Beta and tmaps
   if nargin < 3
diff --git a/src/workflows/bidsCopyRawFolder.m b/src/workflows/bidsCopyRawFolder.m
index fb75608d..230eeb98 100644
--- a/src/workflows/bidsCopyRawFolder.m
+++ b/src/workflows/bidsCopyRawFolder.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function bidsCopyRawFolder(opt, deleteZippedNii, modalitiesToCopy, unZip)
   %
   % Copies the folders from the ``raw`` folder to the
@@ -25,6 +23,7 @@ function bidsCopyRawFolder(opt, deleteZippedNii, modalitiesToCopy, unZip)
   % :param unZip:
   % :type unZip: boolean
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   %% input variables default values
 
diff --git a/src/workflows/bidsCreateROI.m b/src/workflows/bidsCreateROI.m
index 2349c503..07127220 100644
--- a/src/workflows/bidsCreateROI.m
+++ b/src/workflows/bidsCreateROI.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function bidsCreateROI(opt)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   if nargin < 1
     opt = [];
@@ -9,7 +9,7 @@ function bidsCreateROI(opt)
   [BIDS, opt] = setUpWorkflow(opt, 'create ROI');
 
   opt.dir.roi = [opt.derivativesDir '-roi'];
-  spm_mkdir(fullfile(opt.roiDir, 'group'));
+  spm_mkdir(fullfile(opt.dir.roi, 'group'));
 
   opt.jobsDir = fullfile(opt.dir.roi, 'JOBS', opt.taskName);
 
@@ -31,7 +31,7 @@ function bidsCreateROI(opt)
   if any(strcmp(opt.roi.space, 'individual'))
 
     roiList = spm_select('FPlist', ...
-                         fullfile(opt.roiDir, 'group'), ...
+                         fullfile(opt.dir.roi, 'group'), ...
                          '^space-.*_mask.nii$');
 
     for iSub = 1:numel(opt.subjects)
@@ -60,7 +60,7 @@ function bidsCreateROI(opt)
       spm_mkdir(opt.dir.roi, ['sub-' subLabel], 'roi');
 
       roiList = spm_select('FPlist', ...
-                           fullfile(opt.roiDir, 'group'), ...
+                           fullfile(opt.dir.roi, 'group'), ...
                            '^wspace.*_mask.nii.*$');
 
       for iROI = 1:size(roiList, 1)
diff --git a/src/workflows/bidsCreateVDM.m b/src/workflows/bidsCreateVDM.m
index 461ed2fe..c235682c 100644
--- a/src/workflows/bidsCreateVDM.m
+++ b/src/workflows/bidsCreateVDM.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsCreateVDM(opt)
   %
   % Creates the voxel displacement maps from the fieldmaps of a BIDS
@@ -20,6 +18,7 @@ function bidsCreateVDM(opt)
   % Inspired from spmup ``spmup_BIDS_preprocess`` (@ commit 198c980d6d7520b1a99)
   % (URL missing)
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'create voxel displacement map');
 
diff --git a/src/workflows/bidsFFX.m b/src/workflows/bidsFFX.m
index 5765e289..ceee4257 100644
--- a/src/workflows/bidsFFX.m
+++ b/src/workflows/bidsFFX.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsFFX(action, opt, funcFWHM)
   %
   % - builds the subject level fMRI model and estimates it.
@@ -27,14 +25,15 @@ function bidsFFX(action, opt, funcFWHM)
   % For unsmoothed data ``funcFWHM = 0``, for smoothed data ``funcFWHM = ... mm``.
   % In this way we can make multiple ffx for different smoothing degrees.
   %
-  
+  % (C) Copyright 2020 CPP_SPM developers
+
   if opt.glm.roibased.do
-      message = sprintf(...
-          ['The option opt.glm.roibased.do is set to true.\n', ...
-           ' Change the option to false to use this workflow or\n', ...
-           ' use the bidsRoiBasedGLM workflow to run roi based GLM.']);
-      error(message);
-  end  
+    message = sprintf( ...
+                      ['The option opt.glm.roibased.do is set to true.\n', ...
+                       ' Change the option to false to use this workflow or\n', ...
+                       ' use the bidsRoiBasedGLM workflow to run roi based GLM.']);
+    error(message);
+  end
 
   [BIDS, opt] = setUpWorkflow(opt, 'subject level GLM');
 
diff --git a/src/workflows/bidsLesionSegmentation.m b/src/workflows/bidsLesionSegmentation.m
index 627cba8e..af0fb8da 100755
--- a/src/workflows/bidsLesionSegmentation.m
+++ b/src/workflows/bidsLesionSegmentation.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function bidsLesionSegmentation(opt)
   %
   % Performs segmentation to detect lesions of anatomical image.
@@ -14,6 +12,7 @@ function bidsLesionSegmentation(opt)
   %
   % Segmentation will be performed using the information provided in the BIDS data set.
   %
+  % (C) Copyright 2021 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'lesion segmentation');
 
diff --git a/src/workflows/bidsRFX.m b/src/workflows/bidsRFX.m
index a735c538..96bc3153 100644
--- a/src/workflows/bidsRFX.m
+++ b/src/workflows/bidsRFX.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsRFX(action, opt, funcFWHM, conFWHM)
   %
   % - smooths all contrast images created at the subject level
@@ -30,6 +28,7 @@ function bidsRFX(action, opt, funcFWHM, conFWHM)
   % - case ``RFX``: Mean Struct, MeanMask, Factorial design specification and
   %   estimation, Contrast estimation
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   if nargin < 4 || isempty(funcFWHM)
     funcFWHM = 0;
diff --git a/src/workflows/bidsRealignReslice.m b/src/workflows/bidsRealignReslice.m
index d2dd05bf..0b90bb8d 100644
--- a/src/workflows/bidsRealignReslice.m
+++ b/src/workflows/bidsRealignReslice.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsRealignReslice(opt)
   %
   % Realigns and reslices the functional data of a given task.
@@ -14,6 +12,7 @@ function bidsRealignReslice(opt)
   %
   % Assumes that ``bidsSTC()`` has already been run.
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'realign and reslice');
 
diff --git a/src/workflows/bidsRealignUnwarp.m b/src/workflows/bidsRealignUnwarp.m
index 5ec1c452..c56387a6 100644
--- a/src/workflows/bidsRealignUnwarp.m
+++ b/src/workflows/bidsRealignUnwarp.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsRealignUnwarp(opt)
   %
   % Realigns and unwarps the functional data of a given task.
@@ -17,6 +15,7 @@ function bidsRealignUnwarp(opt)
   % If the ``bidsCreateVDM()`` workflow has been run before the voxel displacement
   % maps will be used unless ``opt.useFieldmaps`` is set to ``false``.
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'realign and unwarp');
 
diff --git a/src/workflows/bidsResliceTpmToFunc.m b/src/workflows/bidsResliceTpmToFunc.m
index 788c971f..3394c54f 100644
--- a/src/workflows/bidsResliceTpmToFunc.m
+++ b/src/workflows/bidsResliceTpmToFunc.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsResliceTpmToFunc(opt)
   %
   % Reslices the tissue probability map (TPMs) from the segmentation to the mean
@@ -20,6 +18,7 @@ function bidsResliceTpmToFunc(opt)
   % as the computation of the tSNR by ``spmup`` requires the TPMs to have the same dimension
   % as the functional.
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'reslicing tissue probability maps to functional dimension');
 
diff --git a/src/workflows/bidsResults.m b/src/workflows/bidsResults.m
index 08497bc6..ae744de4 100644
--- a/src/workflows/bidsResults.m
+++ b/src/workflows/bidsResults.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsResults(opt, funcFWHM, conFWHM)
   %
   % Computes the results for a series of contrast that can be
@@ -20,6 +18,7 @@ function bidsResults(opt, funcFWHM, conFWHM)
   %                 images (Gaussian kernel size).
   % :type conFWHM: scalar
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'computing GLM results');
 
diff --git a/src/workflows/bidsRoiBasedGLM.m b/src/workflows/bidsRoiBasedGLM.m
index fdc02688..948a5a96 100644
--- a/src/workflows/bidsRoiBasedGLM.m
+++ b/src/workflows/bidsRoiBasedGLM.m
@@ -1,15 +1,18 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function bidsRoiBasedGLM(opt)
   %
+  % Will run a GLM within a ROI using MarsBar.
+  %
+  % Will compute the percent signal change and the time course of the events
+  % or blocks of contrast specified in the BIDS model.
   %
-  
+  % (C) Copyright 2021 CPP_SPM developers
+
   if ~opt.glm.roibased.do
-      message = sprintf(...
-          ['The option opt.glm.roibased.do is set to false.\n', ...
-           ' Change the option to true to use this workflow or\n', ...
-           ' use the bidsFFX workflow to run whole brain GLM.']);
-      error(message);
+    message = sprintf( ...
+                      ['The option opt.glm.roibased.do is set to false.\n', ...
+                       ' Change the option to true to use this workflow or\n', ...
+                       ' use the bidsFFX workflow to run whole brain GLM.']);
+    error(message);
   end
 
   funcFWHM = 0;
diff --git a/src/workflows/bidsSTC.m b/src/workflows/bidsSTC.m
index 58aaf908..76c19eb5 100644
--- a/src/workflows/bidsSTC.m
+++ b/src/workflows/bidsSTC.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function bidsSTC(opt)
   %
   % Performs the slie timing correction of the functional data.
@@ -29,6 +27,7 @@ function bidsSTC(opt)
   %
   % See the documentation for more information about slice timing correction.
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'slice timing correction');
 
diff --git a/src/workflows/bidsSegmentSkullStrip.m b/src/workflows/bidsSegmentSkullStrip.m
index d990bba3..978e2b0c 100644
--- a/src/workflows/bidsSegmentSkullStrip.m
+++ b/src/workflows/bidsSegmentSkullStrip.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsSegmentSkullStrip(opt)
   %
   % Segments and skullstrips the anatomical image.
@@ -12,6 +10,7 @@ function bidsSegmentSkullStrip(opt)
   %             ``checkOptions()`` and ``loadAndCheckOptions()``.
   % :type opt: structure
   %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'segmentation and skulltripping');
 
diff --git a/src/workflows/bidsSmoothing.m b/src/workflows/bidsSmoothing.m
index 05f52964..ceaa5710 100644
--- a/src/workflows/bidsSmoothing.m
+++ b/src/workflows/bidsSmoothing.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
-
 function bidsSmoothing(funcFWHM, opt)
   %
   % This performs smoothing to the functional data using a full width
@@ -7,7 +5,7 @@ function bidsSmoothing(funcFWHM, opt)
   %
   % USAGE::
   %
-  %  bidsSmoothing(funcFWHM, [opt])
+  %   bidsSmoothing(funcFWHM, [opt])
   %
   % :param funcFWHM: How much smoothing was applied to the functional
   %                  data in the preprocessing (Gaussian kernel size).
@@ -15,6 +13,8 @@ function bidsSmoothing(funcFWHM, opt)
   % :param opt: structure or json filename containing the options. See
   %             ``checkOptions()`` and ``loadAndCheckOptions()``.
   % :type opt: structure
+  %
+  % (C) Copyright 2020 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'smoothing functional data');
 
diff --git a/src/workflows/bidsSpatialPrepro.m b/src/workflows/bidsSpatialPrepro.m
index e3a4948d..b144192c 100644
--- a/src/workflows/bidsSpatialPrepro.m
+++ b/src/workflows/bidsSpatialPrepro.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function bidsSpatialPrepro(opt)
   %
   % Performs spatial preprocessing of the functional and structural data.
@@ -37,6 +35,7 @@ function bidsSpatialPrepro(opt)
   %
   %  - average T1s across sessions if necessarry
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   [BIDS, opt] = setUpWorkflow(opt, 'spatial preprocessing');
 
diff --git a/src/workflows/saveAndRunWorkflow.m b/src/workflows/saveAndRunWorkflow.m
index d6972712..e652ca6e 100644
--- a/src/workflows/saveAndRunWorkflow.m
+++ b/src/workflows/saveAndRunWorkflow.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function saveAndRunWorkflow(matlabbatch, batchName, opt, subLabel)
   %
   % Saves the SPM matlabbatch and runs it
@@ -17,6 +15,8 @@ function saveAndRunWorkflow(matlabbatch, batchName, opt, subLabel)
   % :type opt: structure
   % :param subID: subject ID
   % :type subID: string
+  %
+  % (C) Copyright 2019 CPP_SPM developers
 
   if nargin < 4
     subLabel = [];
diff --git a/src/workflows/setUpWorkflow.m b/src/workflows/setUpWorkflow.m
index d79ffb29..85fd5e85 100644
--- a/src/workflows/setUpWorkflow.m
+++ b/src/workflows/setUpWorkflow.m
@@ -1,5 +1,3 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
-
 function [BIDS, opt] = setUpWorkflow(opt, workflowName)
   %
   % Calls some common functions to:
@@ -24,6 +22,7 @@
   %           - :opt: options checked
   %           - :group:
   %
+  % (C) Copyright 2019 CPP_SPM developers
 
   opt = loadAndCheckOptions(opt);
 
diff --git a/tests/README.md b/tests/README.md
index dfeb791c..9a2931f3 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -7,57 +7,27 @@ If you are not sure what unit and integration tests are, check the excellent
 chapter about that in the
 [Turing way](https://the-turing-way.netlify.app/reproducible-research/testing.html).
 
-## How to run the tests
-
-### Install MoxUnit
-
-You need to install
-[MOxUnit for matlab and octave](https://github.com/MOxUnit/MOxUnit) to run the
-tests.
-
-Note the install procedure will require you to have
-[git](https://git-scm.com/downloads) installed on your computer. If you don't,
-you can always download the MoxUnit code with this
-[link](https://github.com/MOxUnit/MOxUnit/archive/master.zip).
-
-Run the following from a terminal in the folder where you want to install
-MOxUnit. The `make install` command will find Matlab / Octave on your system and
-make sure it plays nice with MoxUnit.
-
-NOTE: only type in the terminal what is after the `$` sign:
-
-```bash
-# get the code for MOxUnit with git
-git clone https://github.com/MOxUnit/MOxUnit.git
-# enter the newly created folder and set up MoxUnit
-cd MOxUnit
-make install
-```
-
-If you want to check the code coverage on your computer, you can also install
-[MOcov for matlab and octave](https://github.com/MOcov/MOcov). Note that this is
-also part of the continuous integration of the bids-matlab, so you don't need to
-do this.
-
-To run the tests, make sure the `tests/utils` folder has bee added to the Matlab
-/ Octave path
+See
+[HERE](https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md#how-to-run-the-tests)
+for general information on how to run the tests.
 
 ## Add helper functions to the path
 
-There are a some help functions you need to add to the Matlab / Octave path to run the tests:
+There are a some help functions you need to add to the Matlab / Octave path to
+run the tests:
 
 ```
 addpath(fullfile('tests', 'utils'))
 ```
 
-### Install the test data
+## Install the test data
 
 You need to run a bash script to create some empty data files:
 
 From within the `tests` folder.
 
 ```
-sh createDummyDataSet.sh 
+sh createDummyDataSet.sh
 ```
 
 ### Run the tests
@@ -72,50 +42,16 @@ moxunit_runtests tests
 moxunit_runtests tests -verbose
 ```
 
-## Adding more tests
-
-You can use the following function template to write more tests.
-
-```matlab
-function test_suite = test_functionToTest()
-    % This top function is necessary for mox unit to run tests.
-    % DO NOT CHANGE IT except to adapt the name of the function.
-    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
+## Adding tests
 
-function test_function_to_test_basic()
+See
+[HERE](https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md#adding-more-tests)
+to add more tests
 
-    %% set up
+### Style guidelines
 
+#### Filenames
 
-    %% data to test against
+-   unit tests names: test*unit*\*
 
-
-    %% test
-    % assertTrue( );
-    % assertFalse( );
-    % assertEqual( );
-
-end
-
-
-function test_function_to_test_other_usecase()
-
-    %% set up
-
-
-    %% data to test against
-
-
-    %% test
-    % assertTrue( );
-    % assertFalse( );
-    % assertEqual( );
-
-end
-
-```
+-   other tests names: test\_\*
diff --git a/tests/miss_hit.cfg b/tests/miss_hit.cfg
index d4c4fc66..684e5239 100644
--- a/tests/miss_hit.cfg
+++ b/tests/miss_hit.cfg
@@ -1,9 +1 @@
-# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
-line_length: 100
 regex_function_name: "(test(_unit){0,1}_[a-z]+|[a-z]+)(([A-Z]){1}[A-Za-z0-9]+)*"
-
-# 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/tests/test_bidsCopyRawFolder.m b/tests/test_bidsCopyRawFolder.m
index a86801ad..b9d6fb4d 100644
--- a/tests/test_bidsCopyRawFolder.m
+++ b/tests/test_bidsCopyRawFolder.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_bidsCopyRawFolder %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_checkOptions.m b/tests/test_checkOptions.m
index 071e62bf..383c71f0 100644
--- a/tests/test_checkOptions.m
+++ b/tests/test_checkOptions.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_checkOptions %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_createAndReturnOnsetFile.m b/tests/test_createAndReturnOnsetFile.m
index d013bc70..6c10563f 100644
--- a/tests/test_createAndReturnOnsetFile.m
+++ b/tests/test_createAndReturnOnsetFile.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_createAndReturnOnsetFile %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_createDefaultModel.m b/tests/test_createDefaultModel.m
index bf08364d..e508f1ba 100644
--- a/tests/test_createDefaultModel.m
+++ b/tests/test_createDefaultModel.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_createDefaultModel %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_getAnatFilename.m b/tests/test_getAnatFilename.m
index 05098182..94e9de88 100644
--- a/tests/test_getAnatFilename.m
+++ b/tests/test_getAnatFilename.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getAnatFilename %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_getBoldFilename.m b/tests/test_getBoldFilename.m
index ee3aa79a..4a84d601 100644
--- a/tests/test_getBoldFilename.m
+++ b/tests/test_getBoldFilename.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getBoldFilename %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_getBoldFilenameForFFX.m b/tests/test_getBoldFilenameForFFX.m
index 63675f46..a6bd762c 100644
--- a/tests/test_getBoldFilenameForFFX.m
+++ b/tests/test_getBoldFilenameForFFX.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getBoldFilenameForFFX %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_getData.m b/tests/test_getData.m
index 6cbd66c4..7a2cbe68 100644
--- a/tests/test_getData.m
+++ b/tests/test_getData.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getData %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_getFFXdir.m b/tests/test_getFFXdir.m
index 1e0c4005..28734ca8 100644
--- a/tests/test_getFFXdir.m
+++ b/tests/test_getFFXdir.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getFFXdir %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_getMeanFuncFilename.m b/tests/test_getMeanFuncFilename.m
index c5bf35ef..5e7de78d 100644
--- a/tests/test_getMeanFuncFilename.m
+++ b/tests/test_getMeanFuncFilename.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getMeanFuncFilename %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_getRFXdir.m b/tests/test_getRFXdir.m
index c59f51a9..2fb709d1 100644
--- a/tests/test_getRFXdir.m
+++ b/tests/test_getRFXdir.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getRFXdir %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_getRealignParamFile.m b/tests/test_getRealignParamFile.m
index a71a9070..2c4fd28e 100644
--- a/tests/test_getRealignParamFile.m
+++ b/tests/test_getRealignParamFile.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getRealignParamFile %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_loadAndCheckOptions.m b/tests/test_loadAndCheckOptions.m
index c06e2bb8..624063e8 100644
--- a/tests/test_loadAndCheckOptions.m
+++ b/tests/test_loadAndCheckOptions.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_loadAndCheckOptions %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
@@ -109,3 +109,14 @@ function test_loadAndCheckOptionsFromSeveralFiles()
   assertEqual(opt, expectedOptions);
 
 end
+
+function test_loadAndCheckOptionsMoAE()
+
+  jsonContent = setOptions('MoAE');
+
+  optionJsonFile = fullfile(pwd, 'cfg', 'options_task-auditory.json');
+  spm_jsonwrite(optionJsonFile, jsonContent);
+
+  opt = loadAndCheckOptions(optionJsonFile);
+
+end
diff --git a/tests/test_modelFiles.m b/tests/test_modelFiles.m
index 1a80e561..6024012b 100644
--- a/tests/test_modelFiles.m
+++ b/tests/test_modelFiles.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_modelFiles %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_saveMatlabBatch.m b/tests/test_saveMatlabBatch.m
index af8327e7..94d956a8 100644
--- a/tests/test_saveMatlabBatch.m
+++ b/tests/test_saveMatlabBatch.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_saveMatlabBatch %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatch3Dto4D.m b/tests/test_setBatch3Dto4D.m
index 53d3eded..cd21d71f 100644
--- a/tests/test_setBatch3Dto4D.m
+++ b/tests/test_setBatch3Dto4D.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatch3Dto4D %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchComputeVDM.m b/tests/test_setBatchComputeVDM.m
index 1f46e1a5..0efe5e5e 100644
--- a/tests/test_setBatchComputeVDM.m
+++ b/tests/test_setBatchComputeVDM.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchComputeVDM %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchCoregistrationFuncToAnat.m b/tests/test_setBatchCoregistrationFuncToAnat.m
index 45589a53..a789212e 100644
--- a/tests/test_setBatchCoregistrationFuncToAnat.m
+++ b/tests/test_setBatchCoregistrationFuncToAnat.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchCoregistrationFuncToAnat %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchFactorialDesign.m b/tests/test_setBatchFactorialDesign.m
index 7be5aff5..e5fcd5ba 100644
--- a/tests/test_setBatchFactorialDesign.m
+++ b/tests/test_setBatchFactorialDesign.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchFactorialDesign %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchImageCalculation.m b/tests/test_setBatchImageCalculation.m
index bc21e0db..0e70d94c 100644
--- a/tests/test_setBatchImageCalculation.m
+++ b/tests/test_setBatchImageCalculation.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchImageCalculation %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchMeanAnatAndMask.m b/tests/test_setBatchMeanAnatAndMask.m
index af30e028..6b15f9fd 100644
--- a/tests/test_setBatchMeanAnatAndMask.m
+++ b/tests/test_setBatchMeanAnatAndMask.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchMeanAnatAndMask %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchNormalizationSpatialPrepro.m b/tests/test_setBatchNormalizationSpatialPrepro.m
index 7abcf8f6..cb505861 100644
--- a/tests/test_setBatchNormalizationSpatialPrepro.m
+++ b/tests/test_setBatchNormalizationSpatialPrepro.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchNormalizationSpatialPrepro %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchRealign.m b/tests/test_setBatchRealign.m
index 7ead8b76..cc48d55c 100644
--- a/tests/test_setBatchRealign.m
+++ b/tests/test_setBatchRealign.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchRealign %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchResults.m b/tests/test_setBatchResults.m
index 4efd602e..490577ae 100644
--- a/tests/test_setBatchResults.m
+++ b/tests/test_setBatchResults.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchResults %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSTC.m b/tests/test_setBatchSTC.m
index 39435854..85817da4 100644
--- a/tests/test_setBatchSTC.m
+++ b/tests/test_setBatchSTC.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSTC %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSaveCoregistrationMatrix.m b/tests/test_setBatchSaveCoregistrationMatrix.m
index 9492e226..b21575b0 100644
--- a/tests/test_setBatchSaveCoregistrationMatrix.m
+++ b/tests/test_setBatchSaveCoregistrationMatrix.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSaveCoregistrationMatrix %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSegmentation.m b/tests/test_setBatchSegmentation.m
index 7304369b..91872c4d 100644
--- a/tests/test_setBatchSegmentation.m
+++ b/tests/test_setBatchSegmentation.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSegmentation %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSelectAnat.m b/tests/test_setBatchSelectAnat.m
index 7edda8c1..083a9c32 100644
--- a/tests/test_setBatchSelectAnat.m
+++ b/tests/test_setBatchSelectAnat.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSelectAnat %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSkullStripping.m b/tests/test_setBatchSkullStripping.m
index 788e0875..921c227f 100644
--- a/tests/test_setBatchSkullStripping.m
+++ b/tests/test_setBatchSkullStripping.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2019 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2019 CPP_SPM developers
 
 function test_suite = test_setBatchSkullStripping %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSmoothConImages.m b/tests/test_setBatchSmoothConImages.m
index 7a3364c9..98357b9c 100644
--- a/tests/test_setBatchSmoothConImages.m
+++ b/tests/test_setBatchSmoothConImages.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSmoothConImages %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSmoothing.m b/tests/test_setBatchSmoothing.m
index ec5f0e2d..f1016267 100644
--- a/tests/test_setBatchSmoothing.m
+++ b/tests/test_setBatchSmoothing.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSmoothing %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSmoothingFunc.m b/tests/test_setBatchSmoothingFunc.m
index de198f1d..564f93ed 100644
--- a/tests/test_setBatchSmoothingFunc.m
+++ b/tests/test_setBatchSmoothingFunc.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSmoothingFunc %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSubjectLevelContrasts.m b/tests/test_setBatchSubjectLevelContrasts.m
index 7995a8ab..e2d3c548 100644
--- a/tests/test_setBatchSubjectLevelContrasts.m
+++ b/tests/test_setBatchSubjectLevelContrasts.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSubjectLevelContrasts %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSubjectLevelGLMSpec.m b/tests/test_setBatchSubjectLevelGLMSpec.m
index 410a9599..94347c23 100644
--- a/tests/test_setBatchSubjectLevelGLMSpec.m
+++ b/tests/test_setBatchSubjectLevelGLMSpec.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSubjectLevelGLMSpec %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setBatchSubjectLevelResults.m b/tests/test_setBatchSubjectLevelResults.m
index b8f4d636..6ca6d728 100644
--- a/tests/test_setBatchSubjectLevelResults.m
+++ b/tests/test_setBatchSubjectLevelResults.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setBatchSubjectLevelResults %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_setFields.m b/tests/test_setFields.m
index dceeb75b..04412fd3 100644
--- a/tests/test_setFields.m
+++ b/tests/test_setFields.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_setFields %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_cleanCrash.m b/tests/test_unit_cleanCrash.m
index ae8cbfbe..55deacc7 100644
--- a/tests/test_unit_cleanCrash.m
+++ b/tests/test_unit_cleanCrash.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_cleanCrash %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_copyGraphWindownOutput.m b/tests/test_unit_copyGraphWindownOutput.m
index b0698f7b..27d603e3 100644
--- a/tests/test_unit_copyGraphWindownOutput.m
+++ b/tests/test_unit_copyGraphWindownOutput.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_copyGraphWindownOutput %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_createDataDictionary.m b/tests/test_unit_createDataDictionary.m
index ba1aeecf..f9bbe888 100644
--- a/tests/test_unit_createDataDictionary.m
+++ b/tests/test_unit_createDataDictionary.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_createDataDictionary %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_createGlmDirName.m b/tests/test_unit_createGlmDirName.m
index c99b3fec..67765e2d 100644
--- a/tests/test_unit_createGlmDirName.m
+++ b/tests/test_unit_createGlmDirName.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2021 CPP_SPM developers
 
 function test_suite = test_unit_createGlmDirName %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_getFuncVoxelDims.m b/tests/test_unit_getFuncVoxelDims.m
index 2e70c5d5..929e0195 100644
--- a/tests/test_unit_getFuncVoxelDims.m
+++ b/tests/test_unit_getFuncVoxelDims.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_getFuncVoxelDims %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_getGrpLevelContrastToCompute.m b/tests/test_unit_getGrpLevelContrastToCompute.m
index 5947e431..368ca7a8 100644
--- a/tests/test_unit_getGrpLevelContrastToCompute.m
+++ b/tests/test_unit_getGrpLevelContrastToCompute.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_getGrpLevelContrastToCompute %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_getInfo.m b/tests/test_unit_getInfo.m
index ec5198ca..6e948881 100644
--- a/tests/test_unit_getInfo.m
+++ b/tests/test_unit_getInfo.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_getInfo %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_getPrefix.m b/tests/test_unit_getPrefix.m
index 27e2e50f..619a9e91 100644
--- a/tests/test_unit_getPrefix.m
+++ b/tests/test_unit_getPrefix.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_getPrefix %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_getSliceOrder.m b/tests/test_unit_getSliceOrder.m
index 379e0ab1..543c141e 100644
--- a/tests/test_unit_getSliceOrder.m
+++ b/tests/test_unit_getSliceOrder.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_getSliceOrder %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_getSubjectList.m b/tests/test_unit_getSubjectList.m
index 880c1d89..fd9a0c8e 100644
--- a/tests/test_unit_getSubjectList.m
+++ b/tests/test_unit_getSubjectList.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_getSubjectList %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_manageWorkersPool.m b/tests/test_unit_manageWorkersPool.m
index b7c6c6f8..159ae73a 100644
--- a/tests/test_unit_manageWorkersPool.m
+++ b/tests/test_unit_manageWorkersPool.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_manageWorkersPool %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_returnDefaultResultsStructure.m b/tests/test_unit_returnDefaultResultsStructure.m
index 8ef9ec10..6e7df827 100644
--- a/tests/test_unit_returnDefaultResultsStructure.m
+++ b/tests/test_unit_returnDefaultResultsStructure.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_returnDefaultResultsStructure %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_returnEmptyModel.m b/tests/test_unit_returnEmptyModel.m
index cb006589..2b8525bb 100644
--- a/tests/test_unit_returnEmptyModel.m
+++ b/tests/test_unit_returnEmptyModel.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_returnEmptyModel %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_setDerivativesDir.m b/tests/test_unit_setDerivativesDir.m
index 4df4a2cc..6cf46f8c 100644
--- a/tests/test_unit_setDerivativesDir.m
+++ b/tests/test_unit_setDerivativesDir.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_setDerivativesDir %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_specifyContrasts.m b/tests/test_unit_specifyContrasts.m
index 373a13c5..01332c50 100644
--- a/tests/test_unit_specifyContrasts.m
+++ b/tests/test_unit_specifyContrasts.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_specifyContrasts %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_unit_validationInputFile.m b/tests/test_unit_validationInputFile.m
index 29ad4135..d76c0537 100644
--- a/tests/test_unit_validationInputFile.m
+++ b/tests/test_unit_validationInputFile.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_unit_validationInputFile %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_utils.m b/tests/test_utils.m
index ec276918..38efe2b1 100644
--- a/tests/test_utils.m
+++ b/tests/test_utils.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_utils %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/test_writeDatasetDescription.m b/tests/test_writeDatasetDescription.m
index a88804f7..af922521 100644
--- a/tests/test_writeDatasetDescription.m
+++ b/tests/test_writeDatasetDescription.m
@@ -1,4 +1,4 @@
-% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+% (C) Copyright 2020 CPP_SPM developers
 
 function test_suite = test_writeDatasetDescription %#ok<*STOUT>
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
diff --git a/tests/utils/defaultOptions.m b/tests/utils/defaultOptions.m
index 5c7211f8..d258de43 100644
--- a/tests/utils/defaultOptions.m
+++ b/tests/utils/defaultOptions.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function expectedOptions = defaultOptions(taskName)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   expectedOptions.sliceOrder = [];
   expectedOptions.STC_referenceSlice = [];
diff --git a/tests/utils/setOptions.m b/tests/utils/setOptions.m
index 9e12acb8..6717eb29 100644
--- a/tests/utils/setOptions.m
+++ b/tests/utils/setOptions.m
@@ -1,6 +1,6 @@
-% (C) Copyright 2021 CPP BIDS SPM-pipeline developers
-
 function opt = setOptions(task, subLabel)
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
   thisDir = fileparts(mfilename('fullpath'));
 
@@ -15,6 +15,9 @@
 
     opt.taskName = 'auditory';
 
+    opt.result.Steps.Contrasts(1).Name = 'listening';
+    opt.result.Steps.Contrasts(2).Name = 'listening_inf_baseline';
+
   else
 
     opt.taskName = task;
diff --git a/version.txt b/version.txt
index 81fd7ba0..60453e69 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-v0.2.0
\ No newline at end of file
+v1.0.0
\ No newline at end of file