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Hello Ducan,

Thanks I had changed FSL_DIR to FSLDIR as you suggested
Now FSL 5.0 is succesfully installed If I write fsl in terminal FSL5.0 GUI opens without error. with no problem in fslview also

I am having specific problems in running certain scripts like fslmaths,cluster, fast please see below

mv@mv-HP-Z210-Workstation:~$ fast
fast: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
mv@mv-HP-Z210-Workstation:~$ fslmaths
fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory
mv@mv-HP-Z210-Workstation:~$ cluster
cluster: error while loading shared libraries: libutils.so: cannot open shared object file: No such file or directory

while scripts like atlasquery and few others are working fine
I doubt thefollowing might br the problem:-

I am using bash (shell script) and there is no mention about FSL_DIR in whole script and my  .bashrc file also don't have any line like /usr/share/fsl/4.1/bin. So why I am getting the warning WARNING: /usr/share/fsl/4.1/bin does not exist. (see below)

I am getting this warning after reinstalling FSL 4.1 in the initial opening of termiinal. Can you mention the reason why?
-------- freesurfer-Linux-centos4-stable-pub-v5.1.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
WARNING: /usr/share/fsl/4.1/bin does not exist.
FSL_DIR           /usr/share/fsl/4.1

Thanking you in anticipation


On Mon, Apr 22, 2013 at 2:10 PM, Duncan Mortimer <[log in to unmask]> wrote:
The environment variable that FSL uses to locate it's files is FSLDIR (without the underscore) - the underscore'd version is Freesurfer's own internal reference to the FSL installation.

You should instead be doing the following in your shell

FSLDIR=/usr/local/fsl/5.0
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

Remove any reference to FSL_DIR in your shell setup as Freesurfer has internal copies of any FSL code it requires

Duncan

On 22 Apr 2013, at 07:49, Himanshu Joshi wrote:

> Hello all,
> I had upgraded my fsl from 4.1 to 5.0
> I had provided latest FSLDIR path to .bashrc
> i.e FSL_DIR=/usr/local/fsl/5.0
> . ${FSL_DIR}/etc/fslconf/fsl.sh
> PATH=${FSL_DIR}/bin:${PATH}
> export FSL_DIR PATH
>
> FSL gui is running properly I had installed fslview4.0 also. no problem in that.
>
> But I doubt there is a problem in terminal because my terminal window starts like this
> -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer
> FSFAST_HOME       /usr/local/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR      /usr/local/freesurfer/subjects
> MNI_DIR           /usr/local/freesurfer/mni
> WARNING: /usr/local/fsl/bin does not exist.
> FSL_DIR           /usr/local/fsl
>
> -----------------------------------------------------------------------------------
>
>
> I am unable to find the file to correct the warning "WARNING: /usr/local/fsl/bin does not exist"
> because in bashrc file this line is not at all incorporated
> and I had provides FSL_DIR=/usr/local/fsl/5.0
>
> but as you can see the terminal still says FSL_DIR=usr/local/fsl
> this error also is not visible in  for root's  -- .bashrc file.
> In which file I have to do changes to clear this issue and where it is located.
>
> Please comment
>
>
>
>
>
>
> --
> Himanshu Joshi
>

--
Duncan A B Mortimer DPhil MChem
                Computing Officer, FMRIB Centre, University of Oxford,
              John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
Tel: (0)1865 222713              email: [log in to unmask]
Personal email (not for IT support): [log in to unmask]



--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html