_____ - CDNI's Brain

Overview

Table of Contents
About

MSI

High-Performance Computing (HPC) Resources
Partitions
Module System
Getting Started
Data Storage/Tracking
S3
Common MSI Roadblocks
NGDR

SLURM

Slurm Commands
Slurm Jobs
Cronjobs
Resource Optimization
fairshare
Queue Optimization

Software Environments

VS Code
Miniconda Environments
Software Versioning
Containers
Virtual Machine

Coding Standards

Best Practices

GitHub

GitHub Beginner's Guide
Common Git Commands
GitHub Tips and Tricks
GitHub History Scrub

BIDS

DICOM to BIDS conversion
BIDS Validation
NORDIC Denoising and BIDS NORDIC Wrapper
BIDS Directory Structure

Before processing

Infant Preprocessing
Defacing
10.5T NHP ABCD BIDS Pipeline Synth
Fast Track QC Comparison (ABCD)
Respiration Rate Settings

Processing

Pipelines
S3 Pipeline Wrappers
Infant Pipeline Documentation
DCAN-infant Templates/Atlases
Running nnUNet Predict
Best Practices

After processing

file-mapper
Precision Mapping Wrapper
Processing Status
Infant Quality Assessment
Analyzing Motion Regressors

Troubleshooting

Troubleshooting and Image Viewing
Testing BIBSnet
Requests and Questions

Quality Control

BrainSwipes

Data Uploads and Transfers

Data Transfers
Transfer ABCC Data to the NGDR

NDA Uploads

Managing Data on the NDA

Lab Resources

Basecamp
Recorded Presentations
UMN Recommended Courses
UMN Computer Installs
ZENODO

Plotting Tools

Figure Maker
Connectivity Matrices
Skinny Plot

Analysis Tools

Cifti Conn Matrix
Seed Map Parcellation Wrapper
Template Matching
F Conn Regression
BWAS
Calculating Rest Minutes Pre- and Post-Motion Correction

PHI

A Quick Guide on Protected Health Information (PHI)

MR Image

MR-Image-Translation

Contributions

Contributors and Papers

THANK YOU FOR USING THE BRAIN

_____

CDNI's Brain

THANK YOU FOR USING THE BRAIN
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