New subject: mk-fieldsign problems

3 Jan 2006


      Hi
I would be really grateful if someone could help me with the problems I am 
having with mk-fieldsign. Even after installing a new version of freesurfer and
making various changes to libraries etc. when i run:
"paint-sess -sf sessid -a rtopy -hemi rh" i get the error below:
tksurfer: run tcl script: mk-fieldsign.tcl
couldn't read file "mk-fieldsign.tcl": no such file or directory
even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which
works fine).
i am running Red Hat Linux release 9 (Shrike) and installed from
freesurfer-Linux-rh9-v2.2.tar.gz
any idea what to do?
thanks again for your help!
Jane
In message 1134599450.17318.34.camel@minerva.nmr.mgh.harvard.edu Nick
Schmansky nicks@nmr.mgh.harvard.edu writes:
...
Jane,
Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does
not use these libraries any more (I think the older -20040218 release
did, however).
Do you have the environment variable ITCL_LIBRARY defined in your
startup .cshrc file?  You can test if it is set by typing (in csh or
tcsh):
env|grep ITCL
If it is set (which it might be, from your older freesurfer
installation), then it should be deleted or commented-out from
your .cshrc (or possibly it was placed in your
$FREESURFER_HOME/SetUpFreeSurfer.csh file).
You can also just type this:
unsetenv ITCL_LIBRARY
and then try tkmedit.
If this is not the problem, can you tell me which OS you are running?
Type:
cat /etc/redhat-release
and
uname -a
A last ditch effort is to install the itcl libs, from this site:
http://rpmfind.net/linux/rpm2html/search.php?query=itcl
But this should not be necessary, as tkmedit that you have does not use
this library (I am truly puzzled why 'ldd' shows that it needs these
libs).
Thanks,
Nick
On Mon, 2005-12-12 at 11:40 +0000, Jane Aspell wrote:
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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 1133802940.21136.14.camel@minerva.nmr.mgh.harvard.edu Nick
Schmansky nicks@nmr.mgh.harvard.edu 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
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get the error:
"error while loading shared libraries: libitk3.2.so: cannot open shared
object
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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*
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tix8.1/
libBLT24.a*        libBLTlite.2.4.dylib*  libtix8.1.8.3.so
libtk.so.0*
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tixConfig.sh
libBLT.2.4.dylib*  libBLTlite.a           libtix8.1.8.4.so
libtkstub8.4.a
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tk8.4/
libBLT.2.dylib*    libtcl8.4.so*          libtixsam8.1.8.4.so  tcl8.4/
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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
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reinstalling the entire (new version) package?
thanks!
jane
In message Pine.LNX.4.62.0512021326490.5676@icebox.nmr.mgh.harvard.edu
Doug
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Greve greve@nmr.mgh.harvard.edu writes:
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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 $
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FAST Version 20031218) has a bug in it (it doesn't make the field sign
map). i
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originally downloaded freesurfer-20040218-Linux.tar.gz (for RedHat 9).
also, can someone also confrim the colour coding is: red=upper
field/fovea,
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blue=horizontal meridian/parafovea, green=lower visual field/periphery?
i can't work out what the overlay threshold settings should be in
tksurfer to
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correctly display the colours to code the retinotopy, is there some
rationale
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for choosing them?
thanks a lot for your help!
Jane
In message
Pine.LNX.4.62.0511280225500.19611@icebox.nmr.mgh.harvard.edu Doug
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Greve greve@nmr.mgh.harvard.edu 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
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>> and i believe i have successfully overlaid the results on my
surfaces and
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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
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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
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eccen
>> and polar to the location of the ring and wedge. is there a map
somewhere
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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
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] Re: mk-fieldsign problems