FSL - Revision history

Jadrian Miles at 21:08, 23 March 2010

2010-03-23T21:08:23Z

← Older revision		Revision as of 21:08, 23 March 2010
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	Once you've set up your shell as above, simply execute <code>fsl</code> on the command line to bring up the FSL GUI, which gives you access to interactive, graphical interfaces to most of FSL's tools.		Once you've set up your shell as above, simply execute <code>fsl</code> on the command line to bring up the FSL GUI, which gives you access to interactive, graphical interfaces to most of FSL's tools.

			[[Category:Diffusion MRI]]
			[[Category:Software]]

Jadrian Miles: /* Getting Started */

2010-03-23T21:07:41Z

Getting Started

← Older revision		Revision as of 21:07, 23 March 2010
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	=== Getting Started ===		=== Getting Started ===

	FSL is installed on the CS Linux machines, but your environment requires some setup before you can use it. The setup is different depending on which command-line shell you use. To check which shell you use, open up a terminal window and type <code>echo $SHELL</code>, then hit enter.		FSL is installed on the CS Linux machines, but your environment requires some setup before you can use it. The setup is different depending on which command-line shell you use. To check which shell you use, open up a terminal window and type <code>echo $SHELL</code>, then hit enter.

	<dl><dt>		<dl><dt>
	If your shell is csh or tcsh		If your shell is csh or tcsh
	<dd><ol><li>		<dd><ol><li>
	Edit the file ".cshrc" in your home directory and add the following lines somewhere above the line that reads <code>if ($?prompt == 0) exit</code>:		Edit the file ".cshrc" in your home directory and add the following lines somewhere above the line that reads <code>if ($?prompt == 0) exit</code>:
	<pre>setenv FSLDIR /usr/share/fsl		<pre>setenv FSLDIR /usr/share/fsl
	source ${FSLDIR}/etc/fslconf/fsl.csh		source ${FSLDIR}/etc/fslconf/fsl.csh
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	If your shell is bash		If your shell is bash
	<dd><ol><li>		<dd><ol><li>
	Edit the file ".bashrc" in your home directory and add the following lines somewhere above the line that reads <code>if [ -z "$PS1" ]; then</code>:		Edit the file ".bashrc" in your home directory and add the following lines somewhere above the line that reads <code>if [ -z "$PS1" ]; then</code>:
	<pre>. /usr/share/fsl/etc/fslconf/fsl.sh</pre>		<pre>. /usr/share/fsl/etc/fslconf/fsl.sh</pre>
	Note that the above line of code begins with a dot and a space; these must be included!		Note that the above line of code begins with a dot and a space; these must be included!

Jadrian Miles at 20:59, 23 March 2010

2010-03-23T20:59:49Z

← Older revision		Revision as of 20:59, 23 March 2010
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	~~#REDIRECT~~ [[3rd Party Diffusion MRI Software]]		'''FSL''' is [[3rd Party Diffusion MRI Software\|diffusion MRI software]] made by FMRIB, the Oxford Centre for Functional MRI of the Brain. "FSL" stands for "FMRIB Software Library" and it includes tools for image viewing, masking, segmentation, and registration, as well as diffusion tensor fitting, analysis, and tractography, both deterministic and probabilistic.

			See [http://www.fmrib.ox.ac.uk/fsl/ the FSL website] for more information about the tools included in FSL.

			=== Getting Started ===

			FSL is installed on the CS Linux machines, but your environment requires some setup before you can use it. The setup is different depending on which command-line shell you use. To check which shell you use, open up a terminal window and type <code>echo $SHELL</code>, then hit enter.

			<dl><dt>
			If your shell is csh or tcsh
			<dd><ol><li>
			Edit the file ".cshrc" in your home directory and add the following lines somewhere above the line that reads <code>if ($?prompt == 0) exit</code>:
			<pre>setenv FSLDIR /usr/share/fsl
			source ${FSLDIR}/etc/fslconf/fsl.csh
			setenv PATH ${FSLDIR}/bin:${PATH}
			setenv FSLTCLSH /usr/bin/tclsh
			setenv FSLWISH /usr/bin/wish</pre>
			</li><li>
			Save the file, exit your shell, and open a new shell.
			</li></ol><dt>
			If your shell is bash
			<dd><ol><li>
			Edit the file ".bashrc" in your home directory and add the following lines somewhere above the line that reads <code>if [ -z "$PS1" ]; then</code>:
			<pre>. /usr/share/fsl/etc/fslconf/fsl.sh</pre>
			Note that the above line of code begins with a dot and a space; these must be included!
			</li><li>
			Save the file, exit your shell, and open a new shell.
			</li></ol></dl>

			=== Running the FSL GUI ===

			Once you've set up your shell as above, simply execute <code>fsl</code> on the command line to bring up the FSL GUI, which gives you access to interactive, graphical interfaces to most of FSL's tools.

Jadrian Miles: Redirecting to 3rd Party Diffusion MRI Software

2008-11-17T21:59:15Z

Redirecting to 3rd Party Diffusion MRI Software

New page

#REDIRECT [[3rd Party Diffusion MRI Software]]