HowTo Pages

HowTos

Working with Computers

The Basics

• How to Ask for Help
• Password Troubles (miles, grid portal, etc)
• Getting a Hoffman2 Account (Applies to the UCLA Grid Portal as well)

Analysis

• Using FSL with the Cluster
• Submitting Matlab scripts to the SGE cluster
• Finding FSL Debug Info
• How to Submit Custom Jobs to the Cluster
• How to have a script wait for jobs before proceeding

UNIX Systems

• Do Some Basic UNIX
• Using Screen (shell management program)
• Common Unix Errors and Solutions
• Unix'sims (Changing passwords, etc.)
• Tar Tutorial Archiving Data on UNIX systems
• Creating SSH Shortcuts Using SSH Config
• UNIX Permissions

Mac OSX

• Available OSX text editors (or why you shouldn't use TextEdit)
• Mount AFP Share
• OSX Defaults Hacks and General Customization Useful custom settings not available otherwise.
• Test Your Disk for Errors in OSX

Grid Portal and Hoffman

• Making directories outside of your $HOME visible in the Grid Portal

Scanning

Find the AC-PC line

Optimize the Flip Angle on gradient echo scans

Alzheimer's Disease Study Scanning Proceedures

Image Processing

• FSL: Common Errors and Solutions
• FSL: Useful commands
• Create a T2 Map
• Install OSX processing tools
• Determine the volume of brain lost in merging multi-subject data sets
• Create a Synthetic Time Series for testing statistical programs
• Convert between file formats using imconvert (note: ImageConvertor will be our new standard.)
• Convert between file formats using ImageConvertor
• Automatically hunt for artifacts with 'Outlier'
• Select, extract or reorder slices using a modified version of imconvert
• Average the responses from Event-Related trials
• Normalize image intensity using EQ
• Use SPM - the Official manual
• Use SPM (a basic brain mapping guide)
• Use SPM (a basic brain mapping guide)
• Do subject-subject registration & Create Your Own Atlas
• Calculate cortical surface area using FreeSurfer
• UCLA Multimodal Connectivity Package
• Run PPI in FSL

Utilities

• Test image stability using P2P
• Edit or create the contents of an analyze image header
• Compress files using SmallTime
• Test for RF Leaks
• Test Devices for Added MRI Noise
• Psychtoolbox
• Using the FileMaker Pro Database for records management

Older Content

Historical pages