Main Page

Welcome to the CCN Lab Wiki.

Terminal Commands & Other Lab Stuff

• New Research Staff
• Lab Roles
• Times when we messed up
• Times when we rocked it
• Participant Screening
• 3D Brain Models

Technobabble

• Setting up a ML Workstation
• UBFS and ubmount
• Using SSH
• Synching Scripts
• Connecting to CCR
• Lab Email
• Excel Formulas
• Troubleshooting
• BASH Tricks
• FreeSurfer on Windows

Data Analysis

• Data Quality
• Downloading CRTC Data
• Behavioral Analyses
• FreeSurfer Pipeline
• SPM Pipeline
• Time Series Analysis
• Network Analyses
• Self-organized-mapping(SOM)
• Data Simulation

Manuscript Preparation

• Brain Rendering in MRIcron (SPM)
• Producing Tables of Coordinates (SPM)
• Extracting XYZ coordinates of .annot labels
• Color schemes (e.g., color keys for graphs, experiment conditions in fMRI renderings, etc.)
  • Above link yoinked from BU's CNR Lab
• Acquisition Parameters at CTRC
• Brain Net Viewer
• Manuscript Formatting

Experiment A to Z (not necessarily in alphabetical order)

• Project-Specific Documentation
• MATLAB Functions
• Participant Triage
• Pre-fMRI Scanning Protocol
• Participant Instructions
• MRI Prep (Prior to scan date)
• MRI Setup
• MIKENET Neural Network C Library Setup
• TensorFlow OpenSource Python Setup
• IDs for Reading Experiment BOLD
• Center for Computational Research (CCR)
• Neural Networks in Python
• Horikawa dataset
  • aws s3 sync --no-sign-request s3://openneuro.org/ds001246 ds001246-download/
• MTA dataset
• Wall of Ideas

Informational

• Developmental Neuroscience
• NSF Proposal Submission Walkthrough for n00bs
• Recipes

MediaWiki - Guides for Getting started

• Useful Formatting Guide
• Configuration settings list
• MediaWiki FAQ
• MediaWiki release mailing list

Consult the User's Guide for information on using the wiki software.