HowTo Pages - Revision history

Ccn admin: 91 revisions

2014-01-16T03:42:59Z

91 revisions

New page

= HowTos =
==Working with Computers==
===Solving Common Errors===
<ul>
<li>[[FileMaker Pro]]</li>
</ul>

===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>
<li>[http://www.mediawiki.org/wiki/Help:Formatting Wiki text formatting]</li>
</ul>

===Sharing===
<ul>
<li>[[DropBox]] or how to share files with many collaborators easily</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>
<li>Hippocampal [[Unfolding]]</li>
<ul><li>[[Segmentation]]</li>
<li>[[Interpolation]]</li>
<li>[[Demarcations]]</li>
<li>[[Calculating thickness]]</li>
</ul>
</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>

===Hoffman2 Cluster===
<ul>
<li>[[ Making directories outside of your $HOME visible in the Grid Portal ]]</li>
<li>[[ Every Day UNIX and Working with Hoffman#Setting up your Bash Profile ]]</li>
<li>[[ How to run WEKA on Hoffman ]]</li>
<li> Jobs </li>
<ul>
<li>[[ How to Submit Custom Jobs to the Cluster ]]</li>
<li>[[ How to have a script wait for jobs before proceeding ]]</li>
<li>[[ Submitting Matlab scripts to the SGE cluster ]]</li>
<li>[[ Parrallelizing_on_Hoffman ]] </li>
</ul>
<li>[[ FAQ#Sun_Grid_Engine ]]</li>
</ul>

== '''Scanning''' ==
[[Find the AC-PC line]]

[[Optimize the Flip Angle on gradient echo scans]]

[[Alzheimer's Disease Study Scanning Proceedures]]

== '''Image Processing''' ==
<ul>
<li>[[FSL: Common Errors and Solutions]]</li>
<li>[[FSL: Useful commands]]</li>
<li>[[Create a T2 Map]]</li>
<li>[[Install OSX processing tools]]</li>
<li>[[Determine the volume of brain lost in merging multi-subject data sets ]]</li>
<li>[[Create a Synthetic Time Series for testing statistical programs]]</li>
<li>[[Convert between file formats using imconvert]] (note: ImageConvertor will be our new standard.)</li>
<li>[[Convert between file formats using ImageConvertor]]</li>
<li>[[Automatically hunt for artifacts with 'Outlier']]</li>
<li>[[Select, extract or reorder slices using a modified version of imconvert]]</li>
<li>[[Average the responses from Event-Related trials]]</li>
<li>[[Normalize image intensity using EQ]]</li>
<li>[http://www.fil.ion.ucl.ac.uk/spm/course/manual/man.htm Use SPM - the Official manual]</li>
<li>[http://airto.bmap.ucla.edu/BMCweb/HowTo/SPM/How2spm.html 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>[[Calculate cortical surface area using FreeSurfer]]</li>
<li>[[UCLA Multimodal Connectivity Package]]</li>
</ul>

== '''Utilities''' ==
<ul>
<li>[[Test image stability using P2P]]</li>
<li>[[Edit or create the contents of an analyze image header]]</li>
<li>[[Compress files using SmallTime]]</li>
<li>[[Test for RF Leaks]]</li>
<li>[[Test Devices for Added MRI Noise]]</li>
<li>[[Using the FileMaker Pro Database for records management]]</li>
</ul>

== '''EEG''' ==
<ul>
<li>All things [[EEG]]</li>
<li>[[Psychtoolbox]] a useful MATLAB toolbox for designing experiments</li>
</ul>

= Older Content =
[http://airto.ccn.ucla.edu/BMCweb/HowTo/index.html Historical pages]

Elau: /* Working with Computers */

2012-02-02T20:25:13Z

Working with Computers

New page

= HowTos =
==Working with Computers==
===Solving Common Errors===
<ul>
<li>[[FileMaker Pro]]</li>
</ul>

===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>
<li>[http://www.mediawiki.org/wiki/Help:Formatting Wiki text formatting]</li>
</ul>

===Sharing===
<ul>
<li>[[DropBox]] or how to share files with many collaborators easily</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>

===Hoffman2 Cluster===
<ul>
<li>[[ Making directories outside of your $HOME visible in the Grid Portal ]]</li>
<li>[[ Every Day UNIX and Working with Hoffman#Setting up your Bash Profile ]]</li>
<li>[[ How to run WEKA on Hoffman ]]</li>
<li> Jobs </li>
<ul>
<li>[[ How to Submit Custom Jobs to the Cluster ]]</li>
<li>[[ How to have a script wait for jobs before proceeding ]]</li>
<li>[[ Submitting Matlab scripts to the SGE cluster ]]</li>
<li>[[ Parrallelizing_on_Hoffman ]] </li>
</ul>
<li>[[ FAQ#Sun_Grid_Engine ]]</li>
</ul>

== '''Scanning''' ==
[[Find the AC-PC line]]

[[Optimize the Flip Angle on gradient echo scans]]

[[Alzheimer's Disease Study Scanning Proceedures]]

== '''Image Processing''' ==
<ul>
<li>[[FSL: Common Errors and Solutions]]</li>
<li>[[FSL: Useful commands]]</li>
<li>[[Create a T2 Map]]</li>
<li>[[Install OSX processing tools]]</li>
<li>[[Determine the volume of brain lost in merging multi-subject data sets ]]</li>
<li>[[Create a Synthetic Time Series for testing statistical programs]]</li>
<li>[[Convert between file formats using imconvert]] (note: ImageConvertor will be our new standard.)</li>
<li>[[Convert between file formats using ImageConvertor]]</li>
<li>[[Automatically hunt for artifacts with 'Outlier']]</li>
<li>[[Select, extract or reorder slices using a modified version of imconvert]]</li>
<li>[[Average the responses from Event-Related trials]]</li>
<li>[[Normalize image intensity using EQ]]</li>
<li>[http://www.fil.ion.ucl.ac.uk/spm/course/manual/man.htm Use SPM - the Official manual]</li>
<li>[http://airto.bmap.ucla.edu/BMCweb/HowTo/SPM/How2spm.html 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>[[Calculate cortical surface area using FreeSurfer]]</li>
<li>[[UCLA Multimodal Connectivity Package]]</li>
<li>[[Run PPI in FSL]]</li>
</ul>

== '''Utilities''' ==
<ul>
<li>[[Test image stability using P2P]]</li>
<li>[[Edit or create the contents of an analyze image header]]</li>
<li>[[Compress files using SmallTime]]</li>
<li>[[Test for RF Leaks]]</li>
<li>[[Test Devices for Added MRI Noise]]</li>
<li>[[Using the FileMaker Pro Database for records management]]</li>
</ul>

== '''EEG''' ==
<ul>
<li>All things [[EEG]]</li>
<li>[[Psychtoolbox]] a useful MATLAB toolbox for designing experiments</li>
</ul>

= Older Content =
[http://airto.ccn.ucla.edu/BMCweb/HowTo/index.html Historical pages]

Elau: /* The Basics */

2011-08-09T23:35:50Z

The Basics

← Older revision		Revision as of 23:35, 9 August 2011
Line 6:		Line 6:
	<li>[[Password Troubles]] (miles, grid portal, etc)</li>		<li>[[Password Troubles]] (miles, grid portal, etc)</li>
	<li>[[Getting a Hoffman2 Account]] (Applies to the UCLA Grid Portal as well)</li>		<li>[[Getting a Hoffman2 Account]] (Applies to the UCLA Grid Portal as well)</li>
			<li>[http://www.mediawiki.org/wiki/Help:Formatting Wiki text formatting]</li>
	</ul>		</ul>

Elau: /* Grid Portal and Hoffman */

2011-08-09T22:51:26Z

Grid Portal and Hoffman

← Older revision		Revision as of 22:51, 9 August 2011
Line 41:		Line 41:
	</ul>		</ul>

	===~~Grid Portal and Hoffman~~===		===Hoffman2 Cluster===
	<ul>		<ul>
	<li>[[ Making directories outside of your $HOME visible in the Grid Portal ]]</li>		<li>[[ Making directories outside of your $HOME visible in the Grid Portal ]]</li>
	<li>[[ ~~Submitting MATLAB jobs~~ to Hoffman ]]</li>		<li>[[ Every Day UNIX and Working with Hoffman#Setting up your Bash Profile ]]</li>
	<li>[[ How to Submit Custom Jobs to the Cluster ]]</li>		<li>[[ How to run WEKA on Hoffman ]]</li>
	<li>[[ How to have a script wait for jobs before proceeding ]]</li>		<li> Jobs </li>
	<li>[[ Submitting Matlab scripts to the SGE cluster ]]</li>		<ul>
			<li>[[ How to Submit Custom Jobs to the Cluster ]]</li>
			<li>[[ How to have a script wait for jobs before proceeding ]]</li>
			<li>[[ Submitting Matlab scripts to the SGE cluster ]]</li>
			</ul>
	<li>[[ FAQ#Sun_Grid_Engine ]]</li>		<li>[[ FAQ#Sun_Grid_Engine ]]</li>
	</ul>		</ul>

Elau: /* Grid Portal and Hoffman */

2011-07-27T18:31:04Z

Grid Portal and Hoffman

← Older revision		Revision as of 18:31, 27 July 2011
Line 44:		Line 44:
	<ul>		<ul>
	<li>[[ Making directories outside of your $HOME visible in the Grid Portal ]]</li>		<li>[[ Making directories outside of your $HOME visible in the Grid Portal ]]</li>
			<li>[[ Submitting MATLAB jobs to Hoffman ]]</li>
			<li>[[ How to Submit Custom Jobs to the Cluster ]]</li>
			<li>[[ How to have a script wait for jobs before proceeding ]]</li>
			<li>[[ Submitting Matlab scripts to the SGE cluster ]]</li>
			<li>[[ FAQ#Sun_Grid_Engine ]]</li>
	</ul>		</ul>

Elau: /* ""EEG"" */

2011-07-15T02:34:35Z

""EEG""

← Older revision		Revision as of 02:34, 15 July 2011
Line 86:		Line 86:
	</ul>		</ul>

	== ""EEG"" ==		== '''EEG''' ==
	<ul>		<ul>
	<li>All things [[EEG]]</li>		<li>All things [[EEG]]</li>

Elau: /* HowTos */

2011-07-15T02:31:57Z

HowTos

← Older revision		Revision as of 02:31, 15 July 2011
Line 6:		Line 6:
	<li>[[Password Troubles]] (miles, grid portal, etc)</li>		<li>[[Password Troubles]] (miles, grid portal, etc)</li>
	<li>[[Getting a Hoffman2 Account]] (Applies to the UCLA Grid Portal as well)</li>		<li>[[Getting a Hoffman2 Account]] (Applies to the UCLA Grid Portal as well)</li>
			</ul>

			===Sharing===
			<ul>
			<li>[[DropBox]] or how to share files with many collaborators easily</li>
	</ul>		</ul>

Line 78:		Line 83:
	<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>[[Using the FileMaker Pro Database for records management]]</li>		<li>[[Using the FileMaker Pro Database for records management]]</li>
	</ul>		</ul>

			== ""EEG"" ==
			<ul>
			<li>All things [[EEG]]</li>
			<li>[[Psychtoolbox]] a useful MATLAB toolbox for designing experiments</li>
			</ul>

	= Older Content =		= Older Content =
	[http://airto.ccn.ucla.edu/BMCweb/HowTo/index.html Historical pages]		[http://airto.ccn.ucla.edu/BMCweb/HowTo/index.html Historical pages]

Elau at 01:26, 7 July 2011

2011-07-07T01:26:16Z

New page

= 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''' ==
[[Find the AC-PC line]]

[[Optimize the Flip Angle on gradient echo scans]]

[[Alzheimer's Disease Study Scanning Proceedures]]

== '''Image Processing''' ==
<ul>
<li>[[FSL: Common Errors and Solutions]]</li>
<li>[[FSL: Useful commands]]</li>
<li>[[Create a T2 Map]]</li>
<li>[[Install OSX processing tools]]</li>
<li>[[Determine the volume of brain lost in merging multi-subject data sets ]]</li>
<li>[[Create a Synthetic Time Series for testing statistical programs]]</li>
<li>[[Convert between file formats using imconvert]] (note: ImageConvertor will be our new standard.)</li>
<li>[[Convert between file formats using ImageConvertor]]</li>
<li>[[Automatically hunt for artifacts with 'Outlier']]</li>
<li>[[Select, extract or reorder slices using a modified version of imconvert]]</li>
<li>[[Average the responses from Event-Related trials]]</li>
<li>[[Normalize image intensity using EQ]]</li>
<li>[http://www.fil.ion.ucl.ac.uk/spm/course/manual/man.htm Use SPM - the Official manual]</li>
<li>[http://airto.bmap.ucla.edu/BMCweb/HowTo/SPM/How2spm.html 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>[[Calculate cortical surface area using FreeSurfer]]</li>
<li>[[UCLA Multimodal Connectivity Package]]</li>
<li>[[Run PPI in FSL]]</li>
</ul>

== '''Utilities''' ==
<ul>
<li>[[Test image stability using P2P]]</li>
<li>[[Edit or create the contents of an analyze image header]]</li>
<li>[[Compress files using SmallTime]]</li>
<li>[[Test for RF Leaks]]</li>
<li>[[Test Devices for Added MRI Noise]]</li>
<li>[[Psychtoolbox]] </li>
<li>[[Using the FileMaker Pro Database for records management]]</li>
</ul>

= Older Content =
[http://airto.ccn.ucla.edu/BMCweb/HowTo/index.html Historical pages]

Mscohen: /* '''Utilities''' */

2006-09-12T00:03:16Z

'''Utilities'''

← Older revision		Revision as of 00:03, 12 September 2006
Line 28:		Line 28:
	<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>[~~http://airto.bmap.ucla.edu/BMCweb/HowTo/SmallTime.html~~ 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>

Mscohen: /* '''Scanning''' */

2006-09-11T23:33:40Z

'''Scanning'''

← Older revision		Revision as of 23:33, 11 September 2006
Line 3:		Line 3:
	== '''Scanning''' ==		== '''Scanning''' ==
	[[Find the AC-PC line]]		[[Find the AC-PC line]]
			[[Optimize the Flip Angle on gradient echo scans]]

	== '''Image Processing''' ==		== '''Image Processing''' ==