yes i already had the file. the one you sent me seemed to be a newer version though, so i ran paint-sess using that, but it gives the same error message.
jane In message <[EMAIL PROTECTED]> Bruce Fischl <[EMAIL PROTECTED]> 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 <[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! > >>> > >>> 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 > >>>>> > >>>>> > >>>> > >>>> > >>> > >>> > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD tel: +44 (0)1865-281606 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
