hi again
we've been trying various things to get mk-fieldsign to work: installing the development version of freesurfer and trying it on a different computer, but we get the same error message. We thought that perhaps mk-fieldsign doesn't have the same access permissions as the other tcl scripts or that it's not actually looking in the same directory as for, e.g. tksurfer.tcl for which it gives the full path:
surfer: using interface /home/jaspell/freesurfer/lib/tcl/tksurfer.tcl Read /home/jaspell/freesurfer/surface_labels.txt, found 95 structures tksurfer: run tcl script: mk-fieldsign.tcl
we are still stuck so would be really grateful for any tips! thanks very much, Jane
In message Pine.LNX.4.62.0601030935040.10958@entry.nmr.mgh.harvard.edu Bruce Fischl fischl@nmr.mgh.harvard.edu writes:
hmmm, do you have it? If not, I've attached a copy.
cheers, Bruc e On Tue, 3 Jan 2006, Jane Aspell wrote:
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:
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
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 Pine.LNX.4.62.0512021326490.5676@icebox.nmr.mgh.harvard.edu
Doug
Greve greve@nmr.mgh.harvard.edu 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
Pine.LNX.4.62.0511280225500.19611@icebox.nmr.mgh.harvard.edu Doug
>> 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
>>>> 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 >>> 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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