Difference between revisions of "Fsl"
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| − | This is about | + | This is an example about [[install]]ing [http://www.fmrib.ox.ac.uk/fsl/fsl/linux.html 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 | ||
<pre> | <pre> | ||
| − | # ls | + | [root@gosia centos]# ls |
| − | fsl-4.1.9- | + | fsl-4.1.9-centos5_64.tar.gz fsl_installer.sh |
| − | + | [root@gosia centos]# bash fsl_installer.sh | |
FSL install script | FSL install script | ||
================== | ================== | ||
| Line 12: | Line 14: | ||
*************************************************************** | *************************************************************** | ||
No FSL tarball specified, assuming you want me to install | No FSL tarball specified, assuming you want me to install | ||
| − | / | + | /root/centos/fsl-4.1.9-centos5_64.tar.gz |
from the current directory. | from the current directory. | ||
*************************************************************** | *************************************************************** | ||
| Line 19: | Line 21: | ||
Checking OS release ... | 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) | |
| − | |||
</pre> | </pre> | ||
| − | + | 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 | ||
| − | = CentOs 6 | + | = TroubleShooting = |
| + | SUSE 12.1 and CentOs 6.0: | ||
<pre> | <pre> | ||
| − | + | # ls | |
| − | fsl-4.1.9- | + | fsl-4.1.9-sources.tar.gz fsl_installer.sh |
| − | + | suse:/home/gosia/src # bash fsl_installer.sh | |
FSL install script | FSL install script | ||
================== | ================== | ||
| Line 44: | Line 52: | ||
*************************************************************** | *************************************************************** | ||
No FSL tarball specified, assuming you want me to install | No FSL tarball specified, assuming you want me to install | ||
| − | / | + | /home/gosia/src/fsl-4.1.9-sources.tar.gz |
from the current directory. | from the current directory. | ||
*************************************************************** | *************************************************************** | ||
| Line 51: | Line 59: | ||
Checking OS release ... | Checking OS release ... | ||
| − | + | [Failed] This is Linux and you have provided a non-Linux build of FSL! | |
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| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
</pre> | </pre> | ||
= See also = | = See also = | ||
* http://www.linuxquestions.org/questions/linux-from-scratch-13/usr-bin-ginstall-doesnt-exist-32513/ - about ginstall | * http://www.linuxquestions.org/questions/linux-from-scratch-13/usr-bin-ginstall-doesnt-exist-32513/ - about ginstall | ||
Latest revision as of 16:56, 21 August 2012
This is an example about installing FSL, tool for brain image analysis.
Contents
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!
