hi nick
when i type >ldd `which tkmedit` i get the ouput pasted below this email.
libitk3.2.so and libitcl3.2.so are not found - could be the problem?
uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh
(and typing 'unsetenv TCLLIBPATH') had no effect.
an earlier version of freesurfer(freesurfer-20040218) didn't give me any of
these problems and tkmedit etc worked fine.
also, does ANYONE know how to interpret the colour coding (for fovea/vertical
meridian etc) produced by the FsFast retinotopy analysis?!
thanks again!
jane
>ldd `which tkmedit`
libtix8.1.8.3.so =>
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000)
libtk8.4.so => /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so
(0x40051000)
libtcl8.4.so =>
/home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000)
libglut.so.3 => /usr/lib/libglut.so.3 (0x401ba000)
libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401ef000)
libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401f8000)
libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x40210000)
libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000)
libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000)
libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x402ab000)
libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x402ef000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x403ce000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0x403ed000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x4042e000)
libz.so.1 => /usr/lib/libz.so.1 (0x4045b000)
libm.so.6 => /lib/tls/libm.so.6 (0x40469000)
libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4048b000)
libc.so.6 => /lib/tls/libc.so.6 (0x42000000)
libitk3.2.so => not found
libitcl3.2.so => not found
libdl.so.2 => /lib/libdl.so.2 (0x4049a000)
libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x4049e000)
libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x404f0000)
libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x404ff000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x405b2000)
/lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000)
In message <[EMAIL PROTECTED]> Nick
Schmansky <[EMAIL PROTECTED]> writes:
> 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
> > >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
>
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