Can you run paint-sess with the -debug option and send us the output?
On Fri, Jan 06, 2006 at 03:36:50PM +0000, Jane Aspell wrote: > 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 > > -- Kevin Teich _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
