Skip to content

Update code_and_data_management.md #99

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Jun 10, 2025
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 9 additions & 3 deletions doc/code_and_data_management.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
## Version control

In the lab we (try) to stick to version control for code with git/github and data with datalad and gin. Somewhere else is already mentioned but repetita iuvant so

1. Install git on your computer
2. Create a GITHUB account and ask to be added to the lab organization [https://github.com/cpp-lln-lab]
3. Make sure you have your SSH key for GITHUB following this tutorial
Expand All @@ -15,6 +16,7 @@ In the lab we (try) to stick to version control for code with git/github and dat

## Data management
for MRI data the lab is moving towards using the BIDS data structure

* bids starter kit
* bids specification

Expand All @@ -29,18 +31,21 @@ Data:

[GIN organization](https://gin.g-node.org/cpp-lln-lab) for source, raw, and preprocessed data for conversion control and sharing

Dataset summary that puts together all the bidsified raw and derivatives repos of the lab and summarize metadata in a table from the GIN repo above:
Dataset summary that puts together all the bidsified raw and derivatives repos of the lab and summarizes metadata in a table from the GIN repo above:

- [website](https://cpp-lln-lab.github.io/Datasets/)
- [Githuba repo CPP_Datasets](https://github.com/cpp-lln-lab/CPP_Datasets)

Datalad superdataset to grab all the repo together (these are submodules in the [Githuba repo CPP_Datasets](https://github.com/cpp-lln-lab/CPP_Datasets):
- https://github.com/cpp-lln-lab/cpp-lln-lab_derivatives
- https://github.com/cpp-lln-lab/cpp-lln-lab_source

- https://github.com/cpp-lln-lab/cpp-lln-lab_derivatives
- https://github.com/cpp-lln-lab/cpp-lln-lab_source

Guidelines to maintain the CPP dataset https://github.com/cpp-lln-lab/dataset_maintenance


Tools:

- https://github.com/cpp-lln-lab/template_datalad_bids-raw
- https://github.com/cpp-lln-lab/CPP_dcm2Bids
- https://github.com/cpp-lln-lab/letswave_bids_import
Expand All @@ -67,6 +72,7 @@ cooked step by step for MacOS users:


Short guidelines:

- not suitable for an “online” usage (eg running analyses within the folder), it is a cloud service so reading and writing is as fast as your internet connection
- Long term storage
- Please, be organized. Imagine that another person in the future will open that folder and make sense of the content in less than 2 minutes
Expand Down