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PennLINC Lab Manual
Lab Basics
Onboarding
Welcome to PennLINC!
Tasks to do before you get here
First day/week tasks
Accounts and systems set-up
Coordinator Specific
Required online trainings
Penn HR Materials
Resources
Meetings
Lab Meetings
Project Meetings
Recurring Meetings
Talks and Seminars
Communication, Collaboration, & Slack
Lab Space
Travel Guidelines
Concur
Computation Basics
SSH Keys
python
Working on CUBIC/PMACS via Visual Code Studio
Best practices for coding for scientific computing
VPNs
Using Containers
Using screen
Informatics Onboarding (Legacy)
CUBIC
Tutorials
Tutorial Template
Regional Quantification
Updating these Docs
Curating ASL Data
Creating BIDS Events TSVs from ITC EPrime Files
Surfaces and Ciftis
InDesign Tutorial
Data Use Agreements Tutorial
Scheduling and Booking Rooms
Common Methods
BigBrain
Generalized Additive Models (GAMs)
Gradients
Haufe Transforms
Meta-analysis
Setup
Database Search
Abstract Screening
Full-text Screening
Data Extraction
ALE
NIMARE
Neurosynth 2.0
NetNeuroTools
NeuroMaps
Neuroimaging Data Processing Tools
Non-negative Matrix Factorization (NMF)
Partial Least Squares (PLS)
Personalized Functional Networks (PFNs)
Ridge Regression
Spin Tests
abagen
Project Workflow
Project Setup
Stages of a Project
Project Reproducibility Guide
Project Documentation
Datasets
Completed Projects
Data Workflows
Datalad
Data Cycle
Getting Static Data
Available Static Datasets
Data Sharing
Archived Documentation
The Way
Fetching Your Data
Curating BIDS Datasets
Running Pipelines with DataLad
Collaboration & Sharing
CUBIC-flywheel
CUBIC-X11GUI
Projects
PMACS
Flywheel
Lab Website
Edit on GitHub
Here are some standard workflows for projects at PennLINC.
Table of contents
Project Setup
Stages of a Project
Project Reproducibility Guide
Project Documentation