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 <[EMAIL PROTECTED]> Nick Schmansky <[EMAIL PROTECTED]> 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! janeldd `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 ortksurfer iget the error: "error while loading shared libraries: libitk3.2.so: cannot open sharedobjectfile: 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.alibtk8.4.so*tix8.1/ libBLT24.a* libBLTlite.2.4.dylib* libtix8.1.8.3.solibtk.so.0*tixConfig.sh libBLT.2.4.dylib* libBLTlite.a libtix8.1.8.4.solibtkstub8.4.atk8.4/ 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 freesurferwithoutreinstalling the entire (new version) package? thanks! jane In message <[EMAIL PROTECTED]>DougGreve <[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 00:53:50greve Exp $FAST Version 20031218) has a bug in it (it doesn't make the field signmap). ioriginally downloaded freesurfer-20040218-Linux.tar.gz (for RedHat 9). also, can someone also confrim the colour coding is: red=upperfield/fovea,blue=horizontal meridian/parafovea, green=lower visual field/periphery? i can't work out what the overlay threshold settings should be intksurfer tocorrectly display the colours to code the retinotopy, is there somerationalefor choosing them? thanks a lot for your help! Jane In message<[EMAIL PROTECTED]> DougGreve <[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 theinstructions at:https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysisand i believe i have successfully overlaid the results on mysurfaces andnowhave two questions: i wasn't able to create the fieldsign with 'paint-sess' because itcouldn't findtksurfer.new. when i run 'surf-sess' i use the flag -old whichforces itto usetksurfer.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 whenviewingeccenand polar to the location of the ring and wedge. is there a mapsomewherethatcan be loaded that tells me what order the colours run from fovea toperipheryand 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
mk-fieldsign.tcl
Description: Tcl script
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