Jane,
This is an unusual error, since tkmedit and tksurfer do not use the ITK
library. To figure out how libitk3.2.so is being referenced, can you
send me the output of this command:
ldd `which tkmedit`
I suspect there is some conflict between the FSL setup and Freesurfer,
as FSL does use ITK, and Freesurfer does not, but performs the FSL setup
(as a convenience to MGH-NMR users). Along this line, one option is to
edit the file FreeSurferEnv.csh (found in your $FREESURFER_HOME) and
comment-out this line:
source ${FSL_DIR}/etc/fslconf/fsl.csh
like this:
# source ${FSL_DIR}/etc/fslconf/fsl.csh
Another option is to type this after sourcing the freesurfer setup file:
unsetenv TCLLIBPATH
This last option is just a guess at a fix though.
Nick
On Mon, 2005-12-05 at 15:37 +0000, Jane Aspell wrote:
> hi
>
> i installed a newer version of freesurfer (using download
> freesurfer-Linux-rh9-v2.2.tar.gz) but when i try and run tkmedit or tksurfer i
> get the error:
>
> "error while loading shared libraries: libitk3.2.so: cannot open shared object
> file: No such file or directory"
>
> this is my output when i source SetUpFreeSurfer.csh:
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /home/jaspell/freesurfer
> FSFAST_HOME /home/jaspell/freesurfer/fsfast
> SUBJECTS_DIR /home/jaspell/freesurfer/subjects
> FUNCTIONALS_DIR /home/jaspell/freesurfer/sessions
> MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin
> MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib
> TCLLIBPATH /home/jaspell/freesurfer/lib/tcltktixblt/lib
> FSL_DIR /usr/local/fsl
>
> and these are the contents of /home/jaspell/freesurfer/lib/tcltktixblt/lib:
>
> blt2.4/ libBLTlite24.a libtclstub8.4.a libtk8.4.so*
> tix8.1/
> libBLT24.a* libBLTlite.2.4.dylib* libtix8.1.8.3.so libtk.so.0*
> tixConfig.sh
> libBLT.2.4.dylib* libBLTlite.a libtix8.1.8.4.so libtkstub8.4.a
> tk8.4/
> libBLT.2.dylib* libtcl8.4.so* libtixsam8.1.8.4.so tcl8.4/
> tkConfig.sh
> libBLT.a* libtcl.so.0* libtix.so.0 tclConfig.sh
>
>
> any idea how to fix it?
>
> i don't suppose there's a way of updating an old version of freesurfer without
> reinstalling the entire (new version) package?
>
> thanks!
>
> jane
>
>
>
>
> In message <[EMAIL PROTECTED]> Doug
> Greve <[EMAIL PROTECTED]> writes:
> >
> > That's a pretty old version. Can you download and install a new version?
> >
> > I actually don't know that much about the interpretation of the color
> > wheel. Maybe Nouchine or Sari can help with this.
> >
> > doug
> >
> >
> > On Fri, 2 Dec 2005, Jane Aspell wrote:
> >
> > > hi again
> > >
> > > i'm still really stuck with my retinotopy analysis as i'm not sure if my
> > > version of paint-sess $Id: paint-sess,v 1.2 2003/08/06 00:53:50 greve Exp
> > > $
> > > FAST Version 20031218) has a bug in it (it doesn't make the field sign
> > > map). i
> > > originally downloaded freesurfer-20040218-Linux.tar.gz (for RedHat 9).
> > >
> > > also, can someone also confrim the colour coding is: red=upper
> > > field/fovea,
> > > blue=horizontal meridian/parafovea, green=lower visual field/periphery?
> > >
> > > i can't work out what the overlay threshold settings should be in
> > > tksurfer to
> > > correctly display the colours to code the retinotopy, is there some
> > > rationale
> > > for choosing them?
> > >
> > > thanks a lot for your help!
> > >
> > > Jane
> > >
> > >
> > > In message <[EMAIL PROTECTED]> Doug
> > > Greve <[EMAIL PROTECTED]> writes:
> > >>
> > >> What version of freesurfer (and paint-sess) are you using? This was a
> > >> problem in some versions about 6 mo ago, but I thought I fixed them
> > >> all.
> > >>
> > >> doug
> > >>
> > >>
> > >>
> > >> On Thu, 24 Nov 2005, Jane Aspell wrote:
> > >>
> > >>> hi again
> > >>> I have been proceeding with the retinotopy analysis using FsFast,
> > > following the
> > >>> instructions at:
> > >>>
> > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
> > >>> and i believe i have successfully overlaid the results on my surfaces
> > >>> and
> > > now
> > >>> have two questions:
> > >>>
> > >>> i wasn't able to create the fieldsign with 'paint-sess' because it
> > > couldn't find
> > >>> tksurfer.new. when i run 'surf-sess' i use the flag -old which forces it
> > > to use
> > >>> tksurfer.old but this doesn't work in the former case. how can i make
> > >>> 'paint-sess' use tksurfer.old and thus create the fieldsign?
> > >>>
> > >>> there are no instructions on how to relate the colours seen when viewing
> > > eccen
> > >>> and polar to the location of the ring and wedge. is there a map
> > >>> somewhere
> > > that
> > >>> can be loaded that tells me what order the colours run from fovea to
> > > periphery
> > >>> and from vertical to horizontal meridian etc.?
> > >>>
> > >>> thanks again for your help!
> > >>>
> > >>> jane
> > >>>
> > >>>
> > >>>
> > >>
> > >> --
> > >> Douglas N. Greve, Ph.D.
> > >> MGH-NMR Center
> > >> [EMAIL PROTECTED]
> > >> Phone Number: 617-724-2358
> > >> Fax: 617-726-7422
> > >>
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > [EMAIL PROTECTED]
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
>
>
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