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
