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]
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