CDNI's Brain🔗

Table of Contents🔗

This handbook outlines key tools and resources used by the Center for Developmental NeuroImaging (CDNI). Topics covered range from using MSI to basecamp tips. For a full list of topics, see the menu to the left. The broad categories as defined as follows:

Section	Content
Overview	Defining the purpose of this documentation and the labs' goals
MSI	General MSI usage tips, mostly focused on storage and access
SLURM	Tips and notes on using SLURM on MSI
Software	Software/coding tools and how to use them
Coding Standards	Best practices for codebase maintenance within the lab
GitHub	GitHub setup, tips, and tricks
Neuroimaging Data	Types of MRI data and BIDS conversion/validation
Before Processing	Any steps the center performs before running processing pipelines (Defacing, NORDIC, motion filtering, etc)
Processing	Running data processing pipelines on MSI (ABCD-BIDS, fMRIPrep, NiBabies, etc)
After Processing	Any steps the lab does after running processing (filemapper, error query, QA, etc)
Troubleshooting	Notes on troubleshooting the center's codebases
Quality Control	Quality control methods within the lab
Analysis Tools	Tools used by the lab to perform various analyses
Data Uploads and Transfers	Moving data within and outside of MSI
Plotting Tools	Tools used by the lab to create various figures
Segmentation Model	How to train nnUNet
MR Image	How to create synthetic images
Lab Resources	Lab recommendations and software used outside of MSI
Contributions	Authors of this documentation and CDNI papers

For questions, suggestions, or to note any errors, post a Github issue.