From Brain Mapping

Contents 1 HowTos 1.1 Working with Computers 1.1.1 The Basics 1.1.2 Analysis 1.1.3 UNIX Systems 1.1.4 Mac OSX 1.1.5 Grid Portal and Hoffman 1.2 Scanning 1.3 Image Processing 1.4 Utilities 1.5 Repairs 2 Older Content

[edit] HowTos

[edit] Working with Computers

[edit] 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)

[edit] 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

[edit] 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

[edit] 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

[edit] Grid Portal and Hoffman

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

[edit] Scanning

Find the AC-PC line Optimize the Flip Angle on gradient echo scans

[edit] 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

[edit] 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

[edit] Repairs

[edit] Older Content

Historical pages