This application will create _SFB_-conform meta data (_meta.json_ files) for all participants in the _participants.tsv_ file of you your study. The _meta.json files_ will include the subjects _ID_, _sex_ and _age_. Moreover it is possible to register a template _meta.json_ file, which values will be adopted into the newly created meta-files.
### Requirements
It is required to have a Java version greater or equal to 1.8.0 installed. You can download the current Java Corretto here: https://docs.aws.amazon.com/de_de/corretto/latest/corretto-11-ug/downloads-list.html
### Participants.tsv format
The _participants.tsv_ has to follow the this [standard](https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files.html#participants-file). Moreover for the conversion at least following fields must be included:
-`participant_id`: The exact name of the subject folder. Usually this is composed of two parts: "sub-" and the _SFB code_. The _SFB code_ will be extracted and used as _Subject ID_. The _SFB code_ cannot contain hyphens.
-`sex`: Sex of the subject (_m\[ale] or f\[emale])_.
-`age`: Age of the subject (in years).
### GUI Usage
Input fields top down:
1. _Study folder:_
Selects the study folder. The study folder is the folder, which contains both the the _participants.tsv_ file and the subject folders.
2. _Use default meta.json (recommended):_
If cecked allows the user the add a template _meta.json_ file. Every newly created meta-file will adopt its values. It is highly recommended to use this feature to enlarge the richness of the _SFB-metadata_.
If not used, meta-files will be empty besides subject-_ID_, _sex_, _age_ and the name of the Study.
1. _meta.json - File chooser:_
Select the template _meta.json_ file.
3. _Convert:_
Starts _meta.json_ creation process. Once finished a pop-up message will inform the user. If subjects defined in the _participants.tsv_ are non existing, a warning message will be displayed.
**Please keep in mind that this application overwrites any already created _meta.json_ files in the subjects modality folders**
### Contact
Author: [Erik Diers](mailto:erik.diers@rub.de)
Contributor: [Marlene Pacharra](mailto:marlene.pacharra@ruhr-uni-bochum.de) and [Tobias Otto](mailto:tobias.otto@rub.de)
Questions to: INF Projekt, [sfb1280data@rub.de](mailto:sfb1280data@rub.de)
## Getting started
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Add your files
-[ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-[ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-[ ] [Set up project integrations](https://gitlab.ruhr-uni-bochum.de/sfb1280/participantstsvconverter/-/settings/integrations)
## Collaborate with your team
-[ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-[ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-[ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
Use the built-in continuous integration in GitLab.
-[ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-[ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-[ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-[ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-[ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
## Name
Choose a self-explaining name for your project.
## Description
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## Badges
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## Visuals
Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
## Installation
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You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
## Authors and acknowledgment
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## Project status
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