Re: [Freesurfer] errors in library in new version of Freesurfer - Freesurfer

6 Jun 2006


      Thanks for the question. Here is the info that I can provide.
(1) When I did 'source' the *.csh, there was no error.
here is the output
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME     /usr/local/freesurfer/fsfast
SUBJECTS_DIR    /usr/local/freesurfer/subjects
FUNCTIONALS_DIR /usr/local/freesurfer/sessions
MINC_BIN_DIR    /usr/local/freesurfer/mni/bin
MINC_LIB_DIR    /usr/local/freesurfer/mni/lib
PERL5LIB        /usr/local/freesurfer/mni/lib/perl5/5.8.5
GSL_DIR         /usr/local/freesurfer/lib/gsl
QTDIR           /usr/lib/qt3
TCLLIBPATH      /usr/local/freesurfer/lib/tcltktixblt/lib
FSL_DIR         /usr/local/freesurfer/fsl
(2) when I did,  ldd 'which mri_convert', it gave me the following error
message.
     ldd: ./which mri_convert: No such file or directory
(3) When I did, however, just 'which mri_convert', it correctly points to
its location, which is
.........../freesurfer/bin/mri_convert.
(4) Freesurfer is running on the latest version of SUSE on a 64-bit machine.
I downloaded an appropriate version of Freesurfer.
Nam.
...
...
...
Nick Schmansky nicks@nmr.mgh.harvard.edu 06/06/06 4:42 PM >>>
What is the output when this is typed:
source $FREESURFER_HOME/SetUpFreeSurfer.csh
and this:
ldd `which mri_convert`
and what OS is this installed on?
On Tue, 2006-06-06 at 15:24 -0400, Joongnam Yang wrote:
...
I installed the new version of Freesurfer by downloading from Freesurfer
Wiki website.
Then, I ran recon-all -subjid subjectname -autorecon1,
and got the following library errors.
Would someone suggest a solution?
Nam.
mri_convert: error while loading shared libraries: libgsl.so.0: cannot
open
...
shar ed object file: No such file or directory
mri_convert: error while loading shared libraries: libgsl.so.0: cannot
open
...
shar ed object file: No such file or directory
strings: 'mritotal:': No such file
strings: 'Command': No such file
strings: 'not': No such file
strings: 'found.': No such file
nu_correct: Command not found.
................. (and much more....)
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