Diff for "FslInformation" - MRC CBU Imaging Wiki
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Before running fsl you need to run 
Before running fsl you need to run
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which is the latest version of fsl at the moment. By running this command you are also using load sharing with any fsl command. If you want to check if you are using the latest version try
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which is the latest version of fsl at the moment. By running this command you are also using load sharing with any fsl command. If you want to check if you are using the latest version try
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== ALIAS suggestions ==

Sometimes the FSL GUIs seem to freeze if launched with the '&' command from a terminal. A simple suggestion to avoid this from happening is to add a couple aliases in your .cshrc file. For example:
= Recent Updates: =
== 2008/12/15 Installed latest FSL ==
Type
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#FSL Aliases
alias fslview 'xterm -e fslview &'
alias fsl 'xterm -e fsl &'
fsl_4.1.2_setup
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to use it[RC]
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(remember to source the .cshrc file after editing it, by typing 'source ~/.cshrc') == 2008/10/6 small FSL patch requested by Mirjana ==
Ask her if you're curious [RC]
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As a result of the aliases when you type 'fsl' in a terminal, it will open a new xterm (on the least busy machine, if you are using the loadbalancing scripts -- see above) and launch from there the FSL GUI. You will then be able to still use the terminal from which you launched the command without the GUI freezing.

You can create any other alias command by replacing 'guiname' with whichever GUI you like in the following command:
== 2008/9/15 FSL patches applied as requested by Eleftherios ==
You may now choose between the patched version
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alias guiname 'xterm -e guiname &' fsl_4.1.0_setup
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and the unpatched one

{{{
fsl_4.1.0_nopatches_setup
}}}
[RC]

== 2008/9/1 and 2008/9/2 Installed FSL 4.1.0 ==
Type

{{{
fsl_4.1.0_setup
}}}
to use it

Fixed, added load sharing wrappers, accidentally deleted fsl3.2, hope no-one need it.

[RC]

== 2008/02/06 Added load balancing to FSL ==
All FSL 4.0.1 commands are now executed with load balancing.

Details... wrote python script /imaging/local/spm/loadshare/runfsl.py which launches an FSL command on the currently least busy machine. Then, /imaging/local/spm/loadshare/fslwrappers.py which makes symbolic links in /imaging/local/linux/bin/fsl-4.01/bin/loadshare/bin

This directory is now added by fsl_4.0.1_setup instead of the one with the actual commands in.

If you wish to run multiple scripts or jobs in parallel launch with separate xterms like this:

{{{
   xterm -e [your command 1] &
   xterm -e [your command 2] &
   e.g., xterm -e feat myscript.fsf &
}}}
[RC, MM]

== 2007/12/12 Added FSL 4.0.1 ==
To use, type

{{{
fsl_4.0.1_setup
}}}
at the Linux prompt

FSL information

FSL is the FMRIB Software Library. It is a C / C++ / Tcl/Tk package written by the Oxford analysis group.

For more information see:

You can find the FSL example data set (http://www.fmrib.ox.ac.uk/fsl/feeds/doc/index.html) in /imaging/local/fsl/feeds.

The data for the FSL course is in /imaging/local/fsl/fslcourse.

Any problems, report them to MartinMonti.

Using the latest version of FSL

Before running fsl you need to run

fsl_4.1.2_setup

which is the latest version of fsl at the moment. By running this command you are also using load sharing with any fsl command. If you want to check if you are using the latest version try

which fsl

Using a specific version of FSL on the CBU systems

If you need to use a specific version, rather than the one pointed to by /imaging/local/linux/bin/fsl, then define the path to the version of FSL you want, and put something like this at the end of your ~/.cshrc file:

# FSL stuff
setenv FSLDIR /imaging/local/linux/bin/fsl-3.3.11
source ${FSLDIR}/etc/fslconf/fsl.csh
set path = (${FSLDIR}/bin $path)

If you want to use the loadsharing system, then replace the last line above with the following:

set path = (${FSLDIR}/bin/loadshare/bin $path)

In order for this to work when you login across linux machines, you will (I'm afraid) also need to put the same lines in your ~/.login file. Put these lines somewhere between the lines #  Space for personal defaults and #  End space for personal defaults in the ~/.login file. By using this method load sharing is not used automatically.

Recent Updates:

2008/12/15 Installed latest FSL

Type

fsl_4.1.2_setup

to use it[RC]

2008/10/6 small FSL patch requested by Mirjana

Ask her if you're curious [RC]

2008/9/15 FSL patches applied as requested by Eleftherios

You may now choose between the patched version

fsl_4.1.0_setup

and the unpatched one

fsl_4.1.0_nopatches_setup

[RC]

2008/9/1 and 2008/9/2 Installed FSL 4.1.0

Type

fsl_4.1.0_setup

to use it

Fixed, added load sharing wrappers, accidentally deleted fsl3.2, hope no-one need it.

[RC]

2008/02/06 Added load balancing to FSL

All FSL 4.0.1 commands are now executed with load balancing.

Details... wrote python script /imaging/local/spm/loadshare/runfsl.py which launches an FSL command on the currently least busy machine. Then, /imaging/local/spm/loadshare/fslwrappers.py which makes symbolic links in /imaging/local/linux/bin/fsl-4.01/bin/loadshare/bin

This directory is now added by fsl_4.0.1_setup instead of the one with the actual commands in.

If you wish to run multiple scripts or jobs in parallel launch with separate xterms like this:

   xterm -e [your command 1] &
   xterm -e [your command 2] &
   e.g., xterm -e feat myscript.fsf &

[RC, MM]

2007/12/12 Added FSL 4.0.1

To use, type

fsl_4.0.1_setup

at the Linux prompt

CbuImaging: FslInformation (last edited 2019-09-11 13:50:27 by MartaCorreia)