[Neurodebian-devel] Problem with library path and libfslvtkio.so

Tue Mar 19 13:22:21 UTC 2013

Hello NeuroDebian Developers,

There has been an email thread on the FSL list that Michael Hanke helped with but hasn't commented on the response recently.  So I thought he might be away from the office at the moment and wondered if one of you could help instead.  As you can see in the thread below, the issue is about the LD_LIBRARY_PATH and I suspect that the user's environment is not setup correctly, but I don't know enough about Debian/Ubuntu setup to help more.  So I'm hoping that one of you can help.  I'm cc'ing the user (Mohammad) in here so that you can communicate directly if necessary, but I'd appreciate being kept in the loop.

Best wishes and thanks for your help,
Mark

Dr Mark Jenkinson
University Research Lecturer
Head of Structural Image Analysis

FMRIB Centre, University of Oxford,
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222782  (fax 222717)

mark at fmrib.ox.ac.uk<mailto:mark at fmrib.ox.ac.uk>  http://www.fmrib.ox.ac.uk/~mark

Hi again

I copied "export LD_LIBRARY_PATH=/usr/share/fsl/5.0/bin:$LD_LIBRARY_PATH" into terminal, and I can run PET and FEAT once. But, for the next time the same problem pops up again. I have to do it everytime I want to use fsl. Do you think it might manipulate the results in anyway?

Thanks
Mohammad

________________________________
From: M.Momenian <momenian21 at YAHOO.COM<mailto:momenian21 at YAHOO.COM>>
To: FSL at JISCMAIL.AC.UK<mailto:FSL at JISCMAIL.AC.UK>
Sent: Friday, March 15, 2013 3:06 PM
Subject: Re: [FSL] libfslvtkio.so error

Hi

I wrote "echo $LD_LIBRARY_PATH" into terminal, but nothing turns out. Should I write something before that or exactly copy the same message? Thanks for your kind reply.

Mohammad
________________________________
From: Michael Hanke <michael.hanke at GMAIL.COM<mailto:michael.hanke at GMAIL.COM>>
To: FSL at JISCMAIL.AC.UK<mailto:FSL at JISCMAIL.AC.UK>
Sent: Friday, March 15, 2013 1:37 PM
Subject: Re: [FSL] libfslvtkio.so<http://libfslvtkio.so/> error

Hi,

this looks good so far. Can you also please post the output of

echo $LD_LIBRARY_PATH

Thanks,

Michael

On Fri, Mar 15, 2013 at 10:17 AM, M.Momenian <momenian21 at yahoo.com<mailto:momenian21 at yahoo.com>> wrote:
Dear David

I ran it in the terminal which came up with the following:

FSLBROWSER=/etc/alternatives/x-www-browser
FSLDIR=/usr/share/fsl/5.0
FSLLOCKDIR=
FSLMACHINELIST=
FSLMULTIFILEQUIT=TRUE
FSLOUTPUTTYPE=NIFTI_GZ
FSLREMOTECALL=
FSLTCLSH=/usr/bin/tclsh
FSLWISH=/usr/bin/wish
I am using windows 7 32 bit. I installed the virtual neurodebian, and then through terminal downloaded fsl. I am working on the problem for a couple of days, but I am exhausted.  I followed all the steps once agian, but it did not work out :( I think the problem is with my OS rather than fsl itself since I surfed the net for the problem and came across with the same problems in Linux. What do you think?

thanks

________________________________
From: David Flitney <flitney at FMRIB.OX.AC.UK<mailto:flitney at FMRIB.OX.AC.UK>>
To: FSL at JISCMAIL.AC.UK<mailto:FSL at JISCMAIL.AC.UK>
Sent: Friday, March 15, 2013 11:19 AM
Subject: Re: [FSL] libfslvtkio.so<http://libfslvtkio.so/> error

Hi,

It sounds like your environment hasn't been set correctly consequently the bundled libraries aren't being found.

Double check that you've followed all the install instructions...
Run "set | grep FSL" and post the output.
Let us know which platform you're running on.

--
Dave Flitney
IT Manager, FMRIB Centre

On 14 Mar 2013, at 19:09, "M.Momenian" <momenian21 at YAHOO.COM<mailto:momenian21 at YAHOO.COM>> wrote:

Dear all

I have just started using fsl recently :) When I want to start BET or FEAT, the following message appears: error while loading shared libraries: libfslvtkio.so<http://libfslvtkio.so/>: cannot open shared object file: No such file or directory. Does anyone know about this error? Thanks in advance

Best
Mohammad

--
Michael Hanke
http://mih.voxindeserto.de
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