CDNI's Brain
Read the Docs
Attention
The Brain is currently under construction. Sections are being reorganized and expanded. Please be patient as we try to improve this handbook.
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 Environments | Coding environments and how to use them |
| Coding Standards | Best practices for codebase maintenance within the lab |
| GitHub | GitHub setup, tips, and tricks |
| BIDS | Anything to convert or validate BIDS data |
| Before Processing | Any steps the center performs before running processing pipelines (ABCD-BIDS, fMRIPrep, NiBabies, etc) |
| Processing | Running data processing pipelines on MSI (ABCD-BIDS, fMRIPrep, NiBabies, etc) |
| After Processing | Any steps the lab does after running processing (ABCD-BIDS, fMRIPrep, NiBabies, etc) |
| Troubleshooting | Notes on troubleshooting the center's codebases |
| Quality Control | Quality control methods within the lab |
| Data Uploads and Transfers | Moving data within and outside of MSI |
| NDA Uploads | Managing data on the NDA |
| Lab Resources | Lab recommendations and software used outside of MSI |
| Plotting Tools | Tools used by the lab to create various figures |
| Analysis Tools | Tools used by the lab to perform various analyses |
| PHI | Quick guide on PHI for a reminder |
| MR Image | How to create synthetic images |
| Contributions | Authors of this documentation and CDNI papers |