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= | = HowTos = | ||
==Working with Computers== | |||
===The Basics=== | |||
<ul> | |||
<li>[[How to Ask for Help]]</li> | |||
<li>[[Password Troubles]] (miles, grid portal, etc)</li> | |||
<li>[[Getting a Hoffman2 Account]] (Applies to the UCLA Grid Portal as well)</li> | |||
</ul> | |||
===Analysis=== | |||
<ul> | |||
<li>[[Using FSL with the Cluster]]</li> | |||
<li>[[Submitting Matlab scripts to the SGE cluster]]</li> | |||
<li>[[Finding FSL Debug Info]]</li> | |||
<li>[[How to Submit Custom Jobs to the Cluster]]</li> | |||
<li>[[How to have a script wait for jobs before proceeding]]</li> | |||
</ul> | |||
===UNIX Systems=== | |||
<ul> | |||
<li>[[Do Some Basic UNIX]]</li> | |||
<li>[[Using Screen]] (shell management program)</li> | |||
<li>[[Common Unix Errors and Solutions]]</li> | |||
<li>[[Unix'sims]] (Changing passwords, etc.)</li> | |||
<li>[[Tar Tutorial]] Archiving Data on UNIX systems</li> | |||
<li>[[Creating SSH Shortcuts Using SSH Config]] | |||
<li>[[UNIX Permissions]]</li> | |||
</ul> | |||
===Mac OSX=== | |||
<ul> | |||
<li>[[Available OSX text editors]] (or why you shouldn't use TextEdit)</li> | |||
<li>[[Mount AFP Share]]</li> | |||
<li>[[OSX Defaults Hacks and General Customization]] Useful custom settings not available otherwise. | |||
<li>[[Test Your Disk for Errors in OSX]]</li> | |||
</ul> | |||
===Grid Portal and Hoffman=== | |||
<ul> | |||
<li>[[ Making directories outside of your $HOME visible in the Grid Portal ]]</li> | |||
</ul> | |||
== '''Scanning''' == | == '''Scanning''' == | ||
[[Find the AC-PC line]] | [[Find the AC-PC line]] | ||
[[Optimize the Flip Angle on gradient echo scans]] | [[Optimize the Flip Angle on gradient echo scans]] | ||
[[Alzheimer's Disease Study Scanning Proceedures]] | |||
== '''Image Processing''' == | == '''Image Processing''' == | ||
<ul> | <ul> | ||
<li>[[FSL: Common Errors and Solutions]]</li> | |||
<li>[[FSL: Useful commands]]</li> | |||
<li>[[Create a T2 Map]]</li> | <li>[[Create a T2 Map]]</li> | ||
<li>[[Install OSX processing tools]]</li> | <li>[[Install OSX processing tools]]</li> | ||
| Line 21: | Line 66: | ||
<li>[http://airto.bmap.ucla.edu/BMCweb/HowTo/SPM_how2.pdf Use SPM (a basic brain mapping guide)]</li> | <li>[http://airto.bmap.ucla.edu/BMCweb/HowTo/SPM_how2.pdf Use SPM (a basic brain mapping guide)]</li> | ||
<li>[http://bishopw.loni.ucla.edu/AIR3/howtosubjects.html Do subject-subject registration & Create Your Own Atlas ]</li> | <li>[http://bishopw.loni.ucla.edu/AIR3/howtosubjects.html Do subject-subject registration & Create Your Own Atlas ]</li> | ||
<li></li> | <li>[[Calculate cortical surface area using FreeSurfer]]</li> | ||
<li>[[UCLA Multimodal Connectivity Package]]</li> | |||
<li>[[Run PPI in FSL]]</li> | |||
</ul> | </ul> | ||
| Line 28: | Line 75: | ||
<li>[[Test image stability using P2P]]</li> | <li>[[Test image stability using P2P]]</li> | ||
<li>[[Edit or create the contents of an analyze image header]]</li> | <li>[[Edit or create the contents of an analyze image header]]</li> | ||
<li>[[ Compress files using SmallTime]]</li> | <li>[[Compress files using SmallTime]]</li> | ||
<li>[[Test for RF Leaks]]</li> | <li>[[Test for RF Leaks]]</li> | ||
<li>[[Test Devices for Added MRI Noise]]</li> | <li>[[Test Devices for Added MRI Noise]]</li> | ||
<li>[[Psychtoolbox]] </li> | |||
<li></li> | <li>[[Using the FileMaker Pro Database for records management]]</li> | ||
</ul> | </ul> | ||
= Older Content = | = Older Content = | ||
[http://airto. | [http://airto.ccn.ucla.edu/BMCweb/HowTo/index.html Historical pages] | ||
Revision as of 01:26, 7 July 2011
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