Hi,
please see here:
http://apsy.gse.uni-magdeburg.de/debian/html/pkgs/fsl.html#usage-information
Michael
On Wed, Apr 01, 2009 at 05:00:01PM +0000, Jayanth Kolar wrote:
> Hi Michael & Others,
>
> Sorry to bother you again. I installed FSL on Ubuntu 8.10(64bit) and all
> went well [The GUI programs are working fine]. But I am not able to run any
> of the command line utilities like fslmaths, fslstats, fnirt, etc. I am
> getting the following errors when I tried different ways to call the command
> line programs:
>
> ubuntu@ubuntu:~/Desktop$ /usr/share/fsl/bin/fslstats
> /usr/share/fsl/bin/fslstats: error while loading shared libraries:
> libnewimage.so: cannot open shared object file: No such file or directory
>
> ubuntu@ubuntu:~/Desktop$ $FSLDIR/bin/fslstats
> bash: /bin/fslstats: No such file or directory
>
> ubuntu@ubuntu:~/Desktop$ fslstats
> bash: fslstats: command not found
>
> Is there a problem with my FSLDIR variable ? I have copied below an extract
> from my FSL configuration file /usr/share/fsl/etc/fslconf/fsl.sh
>
> #### Set up standard FSL user environment variables ####
>
> # Debian has a fixed FSLDIR
> FSLDIR=/usr/share/fsl
> export FSLDIR
>
> # Possum is installed in the same directory
> POSSUMDIR=$FSLDIR
> export POSSUMDIR
>
> # add the fsl binary path to the search path
> PATH=$PATH:/usr/lib/fsl
> export PATH
>
>
> Please let me know how I can set this right. Thanks.
>
> Sincerely,
> Jayanth.
>
> On Tue, Mar 31, 2009 at 6:34 PM, Michael Hanke <[log in to unmask]>wrote:
>
> > On Tue, Mar 31, 2009 at 06:21:50PM +0000, Jayanth Kolar wrote:
> > > Hi Michael,
> > >
> > > I am attaching the 'source.list' file. If that is the case , how can I
> > > enable the 'universe' repositories ?
> >
> > It is the case. Just remove the '#' characters in the beginning of the
> > lines. *BUT* only remove _one_ of them -- even if there are two!
> >
> > Afterwards update the package list and install fsl as you have done
> > before.
> >
> >
> > Michael
> >
> > > On Tue, Mar 31, 2009 at 6:07 PM, Michael Hanke <[log in to unmask]
> > >wrote:
> > >
> > > > Hi,
> > > >
> > > > can you please post the content of your /etc/apt/sources.list file?
> > > >
> > > > I suspect that you haven't enabled Ubuntu's 'universe' repositories.
> > > >
> > > > Michael
> > > >
> > > >
> > > >
> > > > On Tue, Mar 31, 2009 at 06:00:53PM +0000, Jayanth Kolar wrote:
> > > > > *Hi Michael,
> > > > >
> > > > > Thanks for the link ! I tried installing as per the instructions in
> > the
> > > > link
> > > > > you provided but was stuck at step 3. (I am getting the dependency
> > error
> > > > > again). A detailed description of the steps I followed are as
> > follows:*
> > > > >
> > > > > 1) downloaded the "Intrepid Ibex" APT-configuration file and moved it
> > > > into
> > > > > /etc/apt/sources.list.d/
> > > > >
> > > > > 2) Typed in the terminal 'sudo aptitude update'
> > > > > Got the message
> > > > > 'Fetched 190B in 0s (243B/s)'
> > > > > 'Reading package lists... Done'
> > > > >
> > > > > 3) I proceeded to install the FSL package:
> > > > >
> > > > > *I typed in 'sudo aptitude install fsl'
> > > > > and I got a message saying that fsl and fslview have unmet
> > dependencies
> > > > and
> > > > > they wont be installed as below*
> > > > >
> > > > > Reading package lists... Done
> > > > > Building dependency tree
> > > > > Reading state information... Done
> > > > > Reading extended state information
> > > > > Initializing package states... Done
> > > > > The following packages are BROKEN:
> > > > > fsl fslview
> > > > > The following NEW packages will be installed:
> > > > > fsl-atlases{a} fsl-doc{a} fslview-doc{a} libaudio2{a} libnifti1{a}
> > > > > libqt3-mt{a} qt3-assistant{a} qt3-doc{a} tcl8.4{a} tk8.4{a}
> > > > > 0 packages upgraded, 12 newly installed, 0 to remove and 285 not
> > > > upgraded.
> > > > > Need to get 118MB of archives. After unpacking 184MB will be used.
> > > > > *The following packages have unmet dependencies:
> > > > > fsl: Depends: libgdchart-gd2-noxpm which is a virtual package. or
> > > > > libgdchart-gd2-xpm which is a virtual package.
> > > > > Depends: libnewmat10ldbl which is a virtual package.
> > > > > Depends: tcsh which is a virtual package. or
> > > > > c-shell which is a virtual package.
> > > > > fslview: Depends: libnewmat10ldbl which is a virtual package.
> > > > > Depends: libqwt4c2 which is a virtual package.
> > > > > Depends: libvtk5 which is a virtual package.
> > > > > Depends: libvtk5-qt3 which is a virtual package.*
> > > > > The following actions will resolve these dependencies:
> > > > >
> > > > > Keep the following packages at their current version:
> > > > > fsl [Not Installed]
> > > > > fslview [Not Installed]
> > > > >
> > > > > Score is -9872
> > > > >
> > > > > Accept this solution? [Y/n/q/?]
> > > > > *
> > > > > Are there additional packages that I need to install first before
> > > > installing
> > > > > FSL ? If so could you kindly let me know what commands (package
> > names) I
> > > > > have to use.
> > > > >
> > > > > Also I need the 64bit version of fsl. Am I using the correct package
> > name
> > > > in
> > > > > 'sudo aptitude install fsl' ?
> > > > >
> > > > > My apologies if my questions are trivial. I am new to linux
> > repositories
> > > > and
> > > > > am not sure whats happening.*
> > > > >
> > > > > *Thanks again,
> > > > > Jayanth*
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Tue, Mar 31, 2009 at 5:16 PM, Michael Hanke <
> > [log in to unmask]>
> > > > > wrote:
> > > > > > Hi,
> > > > > >
> > > > > > On Tue, Mar 31, 2009 at 04:59:19PM +0000, Jayanth Kolar wrote:
> > > > > >> Hi Matt,
> > > > > >>
> > > > > >> Thanks for the quick reply ! When i try to install
> > > > > >> "fsl_4.1.2.2~intrepid.apsy1_amd64.deb" using the GDebi Package
> > > > > >> Installer I am getting the following error
> > > > > >>
> > > > > >> Error: Dependency is not satisfiable:
> > > > > libgdchart-gd2-noxpm|libgdcahrt-gd2-xpm
> > > > > >>
> > > > > >> I am newbie to linux package installations. Could you kindly let
> > me
> > > > > >> know whats going wrong?
> > > > > >
> > > > > > It looks like you have downloaded the package (.deb) manually. I'm
> > not
> > > > > > familiar with this Gdebi tool. Please take a look at this page:
> > > > > >
> > > > > > http://apsy.gse.uni-magdeburg.de/debian/html/
> > > > > >
> > > > > > Does that make sense?
> > > > > >
> > > > > > Michael
> > > > > >
> > > > > >
> > > > > > --
> > > > > > GPG key: 1024D/3144BE0F Michael Hanke
> > > > > > http://apsy.gse.uni-magdeburg.de/hanke
> > > > > > ICQ: 48230050
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Jayanth Kolar
> > > > > Graduate Research Assistant
> > > > > Physiological Imaging and Modeling Lab
> > > > > University of Illinois at Chicago
> > > > > Chicago IL - 60607
> > > > > 1-408-398-0097
> > > >
> > > > --
> > > > GPG key: 1024D/3144BE0F Michael Hanke
> > > > http://apsy.gse.uni-magdeburg.de/hanke
> > > > ICQ: 48230050
> > > >
> > >
> > >
> > >
> > > --
> > > Jayanth Kolar
> > > Graduate Research Assistant
> > > Physiological Imaging and Modeling Lab
> > > University of Illinois at Chicago
> > > Chicago IL - 60607
> > > 1-408-398-0097
> >
> >
> >
> > --
> > GPG key: 1024D/3144BE0F Michael Hanke
> > http://apsy.gse.uni-magdeburg.de/hanke
> > ICQ: 48230050
> >
>
>
>
> --
> Jayanth Kolar
> Graduate Research Assistant
> Physiological Imaging and Modeling Lab
> University of Illinois at Chicago
> Chicago IL - 60607
> 1-408-398-0097
--
GPG key: 1024D/3144BE0F Michael Hanke
http://apsy.gse.uni-magdeburg.de/hanke
ICQ: 48230050
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