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= HowTos = | = HowTos = | ||
==Working with Computers== | ==Working with Computers== | ||
===Solving Common Errors=== | |||
<ul> | |||
<li>[[FileMaker Pro]]</li> | |||
</ul> | |||
===The Basics=== | ===The Basics=== | ||
<ul> | <ul> | ||
| Line 21: | Line 26: | ||
<li>[[How to Submit Custom Jobs to the Cluster]]</li> | <li>[[How to Submit Custom Jobs to the Cluster]]</li> | ||
<li>[[How to have a script wait for jobs before proceeding]]</li> | <li>[[How to have a script wait for jobs before proceeding]]</li> | ||
<li>Hippocampal [[Unfolding]]</li> | |||
<ul><li>[[Segmentation]]</li> | |||
<li>[[Interpolation]]</li> | |||
<li>[[Demarcations]]</li> | |||
<li>[[Calculating thickness]]</li> | |||
</ul> | |||
</ul> | </ul> | ||
| Line 52: | Line 63: | ||
<li>[[ How to have a script wait for jobs before proceeding ]]</li> | <li>[[ How to have a script wait for jobs before proceeding ]]</li> | ||
<li>[[ Submitting Matlab scripts to the SGE cluster ]]</li> | <li>[[ Submitting Matlab scripts to the SGE cluster ]]</li> | ||
<li>[[ Parrallelizing_on_Hoffman ]] </li> | |||
</ul> | </ul> | ||
<li>[[ FAQ#Sun_Grid_Engine ]]</li> | <li>[[ FAQ#Sun_Grid_Engine ]]</li> | ||
| Line 83: | Line 95: | ||
<li>[[Calculate cortical surface area using FreeSurfer]]</li> | <li>[[Calculate cortical surface area using FreeSurfer]]</li> | ||
<li>[[UCLA Multimodal Connectivity Package]]</li> | <li>[[UCLA Multimodal Connectivity Package]]</li> | ||
</ul> | </ul> | ||
Latest revision as of 03:42, 16 January 2014
HowTos
Working with Computers
Solving Common Errors
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)
- Wiki text formatting
Sharing
- DropBox or how to share files with many collaborators easily
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
- Hippocampal Unfolding
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
Hoffman2 Cluster
- Making directories outside of your $HOME visible in the Grid Portal
- Every Day UNIX and Working with Hoffman#Setting up your Bash Profile
- How to run WEKA on Hoffman
- Jobs
- How to Submit Custom Jobs to the Cluster
- How to have a script wait for jobs before proceeding
- Submitting Matlab scripts to the SGE cluster
- Parrallelizing_on_Hoffman
- FAQ#Sun_Grid_Engine
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
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
- Using the FileMaker Pro Database for records management
EEG
- All things EEG
- Psychtoolbox a useful MATLAB toolbox for designing experiments