HowTo Pages
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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
Scanning
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