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FSL  April 2013

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Subject:

Re: Regarding installation of fsl 5.0

From:

Duncan Mortimer <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 23 Apr 2013 08:50:08 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (170 lines)

(1) You should re-install Ubuntu as the 64 bit version - you will not be able to reliably analyse large datasets on a 32 bit linux install
(2) The .bash(rc/_profile) settings detailed here are specific to Centos/RedHat installs of FSL. Ubuntu installs have a slightly different setup. See this web page for instructions on setup:

http://neuro.debian.net/debian/extracts/fsl/README.Debian


On 23 Apr 2013, at 09:26, Himanshu Joshi wrote:

> UBUNTU 32 bit on 64 bit machine
> 
> 
> 
> 
> On Tue, Apr 23, 2013 at 1:55 PM, Himanshu Joshi <[log in to unmask]> wrote:
> UBUNTU 12.04
> 
> 
> 
> On Tue, Apr 23, 2013 at 1:40 PM, Duncan Mortimer <[log in to unmask]> wrote:
> What brand of Linux is this running on?
> 
> Duncan
> On 23 Apr 2013, at 06:57, Himanshu Joshi wrote:
> 
> > 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
> 
> --
> 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
> 
> 
> 
> -- 
> Himanshu Joshi
> M.Tech. Cognitive & Neuroscience.
> Senior Research Fellow
> Department of Psychiatry
> NIMHANS, Bangalore
> 
> http://mbial.weebly.com/himanshu-joshi.html

-- 
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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