Difference between revisions of "Fsl"

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This is an example about [[install]]ing [http://www.fmrib.ox.ac.uk/fsl/fsl/linux.html FSL], tool for brain image analysis.
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 +
= get it =
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* get a server in the internet e.g. from [[rackspace]]. As operating system, choose CentOS 6.
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* download fsl_installer.sh and fsl-4.1.9-centos5_64.tar.gz
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<pre>
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[root@gosia centos]# ls
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fsl-4.1.9-centos5_64.tar.gz  fsl_installer.sh
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[root@gosia centos]# bash fsl_installer.sh
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FSL install script
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==================
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 +
Looking for FSL tarball in the current directory...
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***************************************************************
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No FSL tarball specified, assuming you want me to install
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/root/centos/fsl-4.1.9-centos5_64.tar.gz
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from the current directory.
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***************************************************************
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 +
Where would you like to install FSL to? [/usr/local]
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 +
Checking OS release ...
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ls: cannot access ld-*.so: No such file or directory
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fsl_installer.sh: line 660: [: -lt: unary operator expected
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fsl_installer.sh: line 663: [: -gt: unary operator expected
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[OK]
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Checking CPU type...
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[OK]
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Checking install file...(this may take several minutes)
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</pre>
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 +
After you have done this, on CentOs 6, you have to
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yum install compat-expat1
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and you must install libjpeg and libtiff.
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 +
== start fsl ==
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You start fsl:
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export FSLDIR=/usr/local/fsl
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. /usr/local/fsl/etc/fslconf/fsl.sh
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/usr/local/fsl/bin/fsl
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 +
= TroubleShooting =
 
SUSE 12.1 and CentOs 6.0:
 
SUSE 12.1 and CentOs 6.0:
 
<pre>
 
<pre>
Line 19: Line 61:
 
[Failed] This is Linux and you have provided a non-Linux build of FSL!
 
[Failed] This is Linux and you have provided a non-Linux build of FSL!
 
</pre>
 
</pre>
Next try
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<pre>
+
= See also =
tar xvzf fsl-4.1.9-sources.tar.gz
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* http://www.linuxquestions.org/questions/linux-from-scratch-13/usr-bin-ginstall-doesnt-exist-32513/ - about ginstall
./build 
 
cat build.log
 
qbootOptions.h:77:27: fatal error: utils/options.h: No such file or directory
 
</pre>
 

Latest revision as of 16:56, 21 August 2012

This is an example about installing FSL, tool for brain image analysis.

get it

  • get a server in the internet e.g. from rackspace. As operating system, choose CentOS 6.
  • download fsl_installer.sh and fsl-4.1.9-centos5_64.tar.gz
[root@gosia centos]# ls
fsl-4.1.9-centos5_64.tar.gz  fsl_installer.sh
[root@gosia centos]# bash fsl_installer.sh 
FSL install script
==================

Looking for FSL tarball in the current directory...
***************************************************************
No FSL tarball specified, assuming you want me to install 
/root/centos/fsl-4.1.9-centos5_64.tar.gz 
from the current directory.
***************************************************************

Where would you like to install FSL to? [/usr/local] 

Checking OS release ...
ls: cannot access ld-*.so: No such file or directory
fsl_installer.sh: line 660: [: -lt: unary operator expected
fsl_installer.sh: line 663: [: -gt: unary operator expected
[OK] 
Checking CPU type...
[OK] 
Checking install file...(this may take several minutes)

After you have done this, on CentOs 6, you have to

yum install compat-expat1

and you must install libjpeg and libtiff.

start fsl

You start fsl:

export FSLDIR=/usr/local/fsl
. /usr/local/fsl/etc/fslconf/fsl.sh 
/usr/local/fsl/bin/fsl

TroubleShooting

SUSE 12.1 and CentOs 6.0:

# ls
fsl-4.1.9-sources.tar.gz  fsl_installer.sh
suse:/home/gosia/src # bash fsl_installer.sh 
FSL install script
==================

Looking for FSL tarball in the current directory...
***************************************************************
No FSL tarball specified, assuming you want me to install 
/home/gosia/src/fsl-4.1.9-sources.tar.gz 
from the current directory.
***************************************************************

Where would you like to install FSL to? [/usr/local] 

Checking OS release ...
[Failed] This is Linux and you have provided a non-Linux build of FSL!

See also