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 <[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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
