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Code and data arrangement

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
  4. Have a look at this doc to have a first idea on how to contribute on github
  5. Have a look around cause we already have a lot of ready to use code ;)
  6. Make sure you are set up with the following tools having a look at this doc’s first section
    1. Datalad (in a nutshell git for data but checkout more here https://handbook.datalad.org/en/latest/)
    2. Gin (host server for data, good for “unlimited” and free cloud back and private and public data sharing)
  7. Ask to be added to the Gin organization of the lab to start storing your data there

Data management

for MRI data the lab is moving towards using the BIDS data structure

  • bids starter kit
  • bids specification

Official GIN/DATALAD CPP dataset organization

[WIP] Checklist to make an official “raw” repo (bids, bids-validator checked, standard CPP data organization (eg group naming, task naming, readme with link to published/preprint, etc))

[WIP - Just dropping useful links here for now]

Data:

Dataset summary (put together all the bidsified raw and derivatives repos of the lab and summarize metadata in a table) https://cpp-lln-lab.github.io/Datasets/ repo to edit it: https://github.com/cpp-lln-lab/Datasets

main organization for "structured": data saving and conversion control and sharing with “raw” (bidsifield) and “derivatives” and “source” repos: https://gin.g-node.org/cpp-lln-lab

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

Datalad superdataset to grab all the repo together: https://github.com/cpp-lln-lab/cpp-lln-lab_derivatives https://github.com/cpp-lln-lab/cpp-lln-lab_source

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 https://github.com/cpp-lln-lab/eeg_bids_conversion

Other back ups

IONS cloud storage

http://sss-intranet.icp.ucl.ac.be/wiki/index.php/Storage_access#Groups

cooked step by step for MacOS users:

  1. Open Finder
  2. Go menu
  3. Element Connect to server
  4. Add address smb://sss-samba.icp.ucl.ac.be/cosy-oc
  5. Use your UCLouvain credentials when asked
  6. Add the opened folder as a favorite (top of the right panel)

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
  • Add README files to help the future user understand what’s inside that folder (e.g. dicoms from the study XXX published in XXX code for conversion/analyses here github.com/xxx, copy of this dataset is also on gin.g-node.org/xxx)

What to put there? Should not become a data dump so not just a new space where a user can free up her/his hard disk

Get organised

Code style guides

matlab https://www.mathworks.com/matlabcentral/fileexchange/46056-matlab-style-guidelines-2-0

Useful links

A quick thread on how to organize your scripts: https://twitter.com/wmvanvliet/status/1240907591791886337