Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

Re: [Freesurfer] Lib prob?
by xmeadow＠uchicago.edu 02 Sep '05

02 Sep '05

Hi, I tried what you said, and after setting up the path and checking that $FREESURFER_HOME/lib/tcltktixblt/bin is at the front of the path I tried running tkmedit <subject> orig. When I did that a window popped up that had 'Medit:' in the title bar. The window had nothing but a gray background. The window stays open for about 7 seconds, and then the title switches from 'Medit:' to the name of the subject, but then the window closes. There are no error messages produced, the window just closes. >Xander ---- Original message ---- >Date: Fri, 02 Sep 2005 15:09:33 -0400 >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Lib prob? >To: Xander Meadow <xmeadow(a)uchicago.edu> >Cc: "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au>, Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > >Xander, > >Can you try executing these two statements after issuing the source >SetUpFreeSurfer.csh command? > > set path = ( $FREESURFER_HOME/lib/tcltktixblt/bin $path ) > rehash > >This will add to the binary search path the location of the tcl-tk-tix- >blt tools. I noticed it is missing from the FreeSurferEnv.csh setup >script. It is possible that the problem you are seeing is because some >of the old tools are being used (from prior installed search paths). > >Can you then try running tkmedit, such as like this: > > tkmedit <subjectname> orig > >(replacing <subjectname> with your subject id). > >Thanks, > >Nick > > >On Fri, 2005-09-02 at 11:39 -0500, Xander Meadow wrote: >> Hi, >> >> Everything was just as you predicted, but I still get the tcl and tk >> errors. >> >> >source freesurfer/dev/SetUpFreeSurfer.csh >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /home/people/xmeadow/freesurfer/dev >> FSFAST_HOME /home/people/xmeadow/freesurfer/dev/fsfast >> SUBJECTS_DIR /home/people/xmeadow/freesurfer/dev/subjects >> FUNCTIONALS_DIR /home/people/xmeadow/freesurfer/dev/sessions >> MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin >> MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib >> PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5 >> >> >> >echo $LD_LIBRARY_PATH >> /usr/pubsw/packages/mni/current/lib:/home/people/xmeadow/freesurfer/ >> dev/lib/tclt >> ktixblt/lib:/home/people/xmeadow/freesurfer/dev/lib/ >> >> > which tkmedit >> /home/people/xmeadow/freesurfer/dev/bin//tkmedit >> >> >ldd `which tkmedit` >> libtix8.1.8.3.so => >> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/ >> lib/libtix8.1.8.3.so (0x005a2000) >> libtk8.4.so => >> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/lib/l >> ibtk8.4.so (0x004c1000) >> libtcl8.4.so => >> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/lib/ >> libtcl8.4.so (0x003b8000) >> libglut.so.3 => /usr/lib/libglut.so.3 (0x007ec000) >> libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x00af8000) >> libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x00b02000) >> libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x00123000) >> libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x00101000) >> libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x00139000) >> libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x001b0000) >> libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x009f9000) >> libgsl.so.0 => /usr/lib/libgsl.so.0 (0x0021e000) >> libgslcblas.so.0 => /usr/lib/libgslcblas.so.0 (0x00382000) >> libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x00dad000) >> libtiff.so.3 => /usr/lib/libtiff.so.3 (0x04a99000) >> libz.so.1 => /usr/lib/libz.so.1 (0x00ad2000) >> libm.so.6 => /lib/tls/libm.so.6 (0x00451000) >> libcrypt.so.1 => /lib/libcrypt.so.1 (0x03e64000) >> libc.so.6 => /lib/tls/libc.so.6 (0x008a3000) >> libdl.so.2 => /lib/libdl.so.2 (0x009f3000) >> libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x00ac2000) >> libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0x003b2000) >> libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x005dc000) >> libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00ce0000) >> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00cd6000) >> libpthread.so.0 => /lib/tls/libpthread.so.0 (0x00ae4000) >> /lib/ld-linux.so.2 (0x0088a000) >> >> Also, I am using the rh9 installation, because it is the latest redhat >> installation available, but the machine is currently running Enterprise >> version 4. >> >> Thanks very much. >> >> >Xander >> >> On Sep 2, 2005, at 10:43 AM, Nick Schmansky wrote: >> >> > Xander, >> > >> > The new download includes the tcl/tk/tix and blt libraries in the >> > $FREESURFER_HOME/lib/tcltktixblt directory, so this freesurfer should >> > not be using any prior installation of tix (such at that in >> > /usr/share). >> > >> > You do not need to delete any prior installations of tix/tcl/tk/blt. >> > The SetUpFreeSurfer.csh script (which calls FreeSurferEnv.csh) will set >> > the LD_LIBRARY_PATH to contain $FREESURFER_HOME/lib/tcltktixblt/lib. >> > You can confirm this setting by typing: >> > >> > env |grep LD_ >> > >> > and checking that the path is found in LD_LIBRARY_PATH. >> > >> > Also, can you run the following commands for me? >> > >> > which tkmedit >> > ldd `which tkmedit` >> > >> > The first will tell you which tkmedit you are using, to confirm that it >> > is the one that you installed. The second command will tell you >> > exactly >> > which libraries tkmedit uses (note: the ` character is not the ' >> > character, rather ` is in the upper left-hand corner of the keyboard, >> > usually). >> > >> > You should see something like this for a rh9 system: >> > >> > [kani:lib] (nmr-dev-env) which tkmedit >> > /usr/local/freesurfer/dev/bin//tkmedit >> > [kani:lib] (nmr-dev-env) ldd `which tkmedit` >> > libtix8.1.8.3.so >> > => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtix8.1.8.3.so >> > (0x40017000) >> > libtk8.4.so >> > => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtk8.4.so >> > (0x40051000) >> > libtcl8.4.so >> > => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtcl8.4.so >> > (0x40111000) >> > libglut.so.3 => /usr/lib/libglut.so.3 (0x401be000) >> > libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401f3000) >> > libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401fc000) >> > libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x40214000) >> > libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x4022a000) >> > libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x40232000) >> > libGL.so.1 => /usr/lib/tls/libGL.so.1 (0x402af000) >> > libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x40318000) >> > libgsl.so.0 => /usr/lib/libgsl.so.0 (0x403f7000) >> > libgslcblas.so.0 => /usr/lib/libgslcblas.so.0 (0x40570000) >> > libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x405a2000) >> > libtiff.so.3 => /usr/lib/libtiff.so.3 (0x405c0000) >> > libz.so.1 => /usr/lib/libz.so.1 (0x40602000) >> > libm.so.6 => /lib/tls/libm.so.6 (0x40610000) >> > libcrypt.so.1 => /lib/libcrypt.so.1 (0x40632000) >> > libc.so.6 => /lib/tls/libc.so.6 (0x42000000) >> > libdl.so.2 => /lib/libdl.so.2 (0x40660000) >> > libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x40664000) >> > libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x406b6000) >> > libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x406c4000) >> > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x40777000) >> > libGLcore.so.1 => /usr/lib/tls/libGLcore.so.1 (0x40780000) >> > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) >> > [kani:lib] (nmr-dev-env) >> > >> > Notice that the tix/tk/tcl libraries are found in the new >> > freesurfer/dev >> > installation path. It is necessary to have consistency among these >> > libraries (BLT is loaded dynamically). >> > >> > I'm curious to know the output of this for your machine. It seems to >> > be >> > difficult for us to predict exactly how a rh9 machine will respond to >> > our install. >> > >> > Thanks! And again, I appreciate your patience! We're trying to make >> > this install easier to use. >> > >> > Nick >> > >> > >> > >> > On Fri, 2005-09-02 at 22:24 +0700, xmeadow(a)uchicago.edu wrote: >> >> Hi, >> >> >> >> I installed the version you recommeneded and I had to make a >> >> few changes (for instance tix8.1 is installed in /usr/share >> >> instead of /usr/lib) on my machine. After creating some soft >> >> links to get around this I started up Freesurfer with the >> >> csurf command, and then inflated a brain. The brain came up >> >> like last time but I'm still getting errors in the logs, and >> >> the tools pallette still doesn't appear. However, Freesurfer >> >> no longer becomes unresponsive, it's just none of the tools >> >> are available. The errors I'm getting are: >> >> >> >> surfer: Error sending tcl command SelectVertex -1: invalid >> >> command name "SelectVertex" >> >> >> >> Whenever I move the mouse over the image of the brain. One >> >> thing to note, I don't have enough room on my /usr partition >> >> so I installed Freesurfer in my home space, but I did change >> >> the FREESURFER_HOME variable in SetUpFreeSurf.csh. Any >> >> thoughts on why I'm still getting tcl errors? Thanks very much. >> >> >> >>> Xander >> >> >> >> ---- Original message ---- >> >>> Date: Thu, 01 Sep 2005 21:30:34 -0400 >> >>> From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >>> Subject: Re: [Freesurfer] Lib prob? >> >>> To: xmeadow(a)uchicago.edu >> >>> Cc: "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au>, >> >> Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> >>> Xander and Alex, >> >>> >> >>> The special rh9 dev release is available now to download at: >> >>> >> >>> http://surfer.nmr.mgh.harvard.edu/pub/dist/ >> >>> >> >>> Look for the file: >> >>> >> >>> freesurfer-Linux-rh9-dev20050901.tar.gz >> >>> >> >>> The installation readme is: >> >>> >> >>> freesurfer-Linux-rh9-dev20050901.README.txt >> >>> >> >>> You will also need the MINC tools if you don't already have them: >> >>> >> >>> mni-Linux2-2.3-i386.tar.gz >> >>> >> >>> and its readme is: >> >>> >> >>> mni-Linux2-README.txt >> >>> >> >>> Nick >> >>> >> >>> >> >>> >> >>> On Fri, 2005-09-02 at 03:33 +0700, xmeadow(a)uchicago.edu wrote: >> >>>> Hi, >> >>>> >> >>>> I downloaded what hopefully is the correct version of blt, and >> >>>> after that ran your script and said everything was fine in >> >>>> terms of libraries. However, I did have to create two soft >> >>>> links. The first one was a softlink from libtix8.1.8.3 to >> >>>> libtix8.1.8.4 in /usr/lib. The second was a softlink from >> >>>> tixwish8.1.8.3 to tixwish8.1.8.4 in /usr/bin. After making >> >>>> both of these changes I was able to run csurf, but when I >> >>>> tried to view an inflated brain the brain image would come up, >> >>>> but then freesurfer freezes and I can't do anything. In the >> >>>> logs I get the following errors: >> >>>> >> >>>> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> >>>> varialble surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >>>> >> >>>> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> >>>> variable tksurfer: run tcl script: /tmp/TmpTclSurf.13311 >> >>>> >> >>>> Unfortunately these error messages mean nothing to me, so I >> >>>> was wondering if anyone else had seen them before. Thanks >> >>>> very much. >> >>>> >> >>>>> Xander >> >>>> >> >>>> >> >>>> >> >>>> ---- Original message ---- >> >>>>> Date: Thu, 01 Sep 2005 11:08:52 -0400 >> >>>>> From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >>>>> Subject: Re: [Freesurfer] Lib prob? >> >>>>> To: xmeadow(a)uchicago.edu, "Fornito, Alexander" >> >>>> <Alexander.Fornito(a)wh.org.au> >> >>>>> Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> >> >>>>> >> >>>>> Alex and Xander, >> >>>>> >> >>>>>> From reading the error messages in your emails, it >> >> appears that >> >>>>> freesurfer is not able to find the tcl/tk, and tix libraries >> >>>> on your >> >>>>> platform. >> >>>>> >> >>>>> We have been working on trying to provide a seamless solution >> >>>> to the >> >>>>> problem of freesurfer finding the external libraries upon >> >>>> which it >> >>>>> depends, on the varied platforms that it supports. >> >>>>> >> >>>>> To help, later today, a new 'dev' build for rh9 that includes >> >>>> many of >> >>>>> the necessary libraries will be posted for download. This is >> >>>> not a >> >>>>> 'stable' release (which is still undergoing testing), but a >> >>>>> 'development' (dev) build, so it is still possible to have >> >>>> installation >> >>>>> problems, but hopefully it will install and work for you. I >> >>>> will email >> >>>>> you again when it is ready, and your patience is appreciated. >> >>>>> >> >>>>> In the meantime, I've attached a script, called >> >>>> 'fs_lib_check', which >> >>>>> will check your system for the libraries that freesurfer >> >>>> requires. I'm >> >>>>> curious to know the results of its output for your systems. >> >>>> Just type >> >>>>> 'fs_lib_check' to run it, and 'fs_lib_check --help' for help >> >>>> text. >> >>>>> >> >>>>> Nick >> >>>>> >> >>>>> >> >>>>> On Thu, 2005-09-01 at 17:06 +1000, Fornito, Alexander wrote: >> >>>>>> Hi, >> >>>>>> We've recently installed the >> >>>> freesurfer-Linux-rh9-dev20050729.tar.gz distribution along >> >>>> with fs_supportlibs.tar.gz. >> >>>>>> csurf works ok, but if i try to run tksurfer, I get the >> >>>> error message below. We'd appreciate any help as we've been >> >>>> stuck for a while. >> >>>>>> Thanks! >> >>>>>> >> >>>>>> tksurfer 1000027 rh white >> >>>>>> surfer: current subjects dir: >> >>>> /data/flanders/work/alex/freesurfer/subjects >> >>>>>> surfer: not in "scripts" dir ==> using cwd for session root >> >>>>>> surfer: session root data dir ($session) set to: >> >>>>>> surfer: /data/flanders/work/alex/freesurfer/subjects >> >>>>>> surfer: Reading header info from >> >>>> >> >> /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info >> >>>>>> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be >> >>>> found. >> >>>>>> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be >> >>>> found. >> >>>>>> surfer: vertices=152190, faces=304376 >> >>>>>> surfer: single buffered window >> >>>>>> Xlib: extension "XFree86-DRI" missing on display ":0.0". >> >>>>>> Tix_Init failed: version conflict for package "Tcl": have >> >>>> 8.3, need 8.4 >> >>>>>> surfer: using interface >> >>>> /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl >> >>>>>> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl >> >>>>>> Reading >> >> /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl >> >>>>>> Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl >> >>>>>> couldn't load file "/usr/lib/libtix8.1.8.4.so": >> >>>> /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No >> >>>> such file or directorysurfer: Error sending tcl command >> >>>> UpdateUndoItemLabel "Nothing to Undo": >> >>>>>> invalid command name "UpdateUndoItemLabel" >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: >> >>>>>> can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_PialVSetLoaded)": no such >> >> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_TimeCourseLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_OverlayLoaded)": no such >> >> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_CurvatureLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_LabelLoaded)": no such variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> >>>> variable >> >>>>>> % surfer: Error sending tcl command MoveToolWindow 663 670: >> >>>>>> invalid command name "MoveToolWindow" >> >>>>>> surfer: Error sending tcl command MoveToolWindow 663 670: >> >>>>>> invalid command name "MoveToolWindow" >> >>>>>> surfer: Error sending tcl command MoveToolWindow 663 670: >> >>>>>> invalid command name "MoveToolWindow" >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> _______________________________________________ >> >>>>>> Freesurfer mailing list >> >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>>>> >> >>>>>> >> >>>>> ________________ >> >>>>> fs_lib_check (4k bytes) >> >>>> >> >>>> >> >>> >> >> >> >> >> > >> >> >

3 3

Re: [Freesurfer] Lib prob?
by xmeadow＠uchicago.edu 02 Sep '05

02 Sep '05

Hi, I installed the version you recommeneded and I had to make a few changes (for instance tix8.1 is installed in /usr/share instead of /usr/lib) on my machine. After creating some soft links to get around this I started up Freesurfer with the csurf command, and then inflated a brain. The brain came up like last time but I'm still getting errors in the logs, and the tools pallette still doesn't appear. However, Freesurfer no longer becomes unresponsive, it's just none of the tools are available. The errors I'm getting are: surfer: Error sending tcl command SelectVertex -1: invalid command name "SelectVertex" Whenever I move the mouse over the image of the brain. One thing to note, I don't have enough room on my /usr partition so I installed Freesurfer in my home space, but I did change the FREESURFER_HOME variable in SetUpFreeSurf.csh. Any thoughts on why I'm still getting tcl errors? Thanks very much. >Xander ---- Original message ---- >Date: Thu, 01 Sep 2005 21:30:34 -0400 >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Lib prob? >To: xmeadow(a)uchicago.edu >Cc: "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au>, Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > >Xander and Alex, > >The special rh9 dev release is available now to download at: > >http://surfer.nmr.mgh.harvard.edu/pub/dist/ > >Look for the file: > >freesurfer-Linux-rh9-dev20050901.tar.gz > >The installation readme is: > >freesurfer-Linux-rh9-dev20050901.README.txt > >You will also need the MINC tools if you don't already have them: > >mni-Linux2-2.3-i386.tar.gz > >and its readme is: > >mni-Linux2-README.txt > >Nick > > > >On Fri, 2005-09-02 at 03:33 +0700, xmeadow(a)uchicago.edu wrote: >> Hi, >> >> I downloaded what hopefully is the correct version of blt, and >> after that ran your script and said everything was fine in >> terms of libraries. However, I did have to create two soft >> links. The first one was a softlink from libtix8.1.8.3 to >> libtix8.1.8.4 in /usr/lib. The second was a softlink from >> tixwish8.1.8.3 to tixwish8.1.8.4 in /usr/bin. After making >> both of these changes I was able to run csurf, but when I >> tried to view an inflated brain the brain image would come up, >> but then freesurfer freezes and I can't do anything. In the >> logs I get the following errors: >> >> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> varialble surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> variable tksurfer: run tcl script: /tmp/TmpTclSurf.13311 >> >> Unfortunately these error messages mean nothing to me, so I >> was wondering if anyone else had seen them before. Thanks >> very much. >> >> >Xander >> >> >> >> ---- Original message ---- >> >Date: Thu, 01 Sep 2005 11:08:52 -0400 >> >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >Subject: Re: [Freesurfer] Lib prob? >> >To: xmeadow(a)uchicago.edu, "Fornito, Alexander" >> <Alexander.Fornito(a)wh.org.au> >> >Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> >> > >> >Alex and Xander, >> > >> >>From reading the error messages in your emails, it appears that >> >freesurfer is not able to find the tcl/tk, and tix libraries >> on your >> >platform. >> > >> >We have been working on trying to provide a seamless solution >> to the >> >problem of freesurfer finding the external libraries upon >> which it >> >depends, on the varied platforms that it supports. >> > >> >To help, later today, a new 'dev' build for rh9 that includes >> many of >> >the necessary libraries will be posted for download. This is >> not a >> >'stable' release (which is still undergoing testing), but a >> >'development' (dev) build, so it is still possible to have >> installation >> >problems, but hopefully it will install and work for you. I >> will email >> >you again when it is ready, and your patience is appreciated. >> > >> >In the meantime, I've attached a script, called >> 'fs_lib_check', which >> >will check your system for the libraries that freesurfer >> requires. I'm >> >curious to know the results of its output for your systems. >> Just type >> >'fs_lib_check' to run it, and 'fs_lib_check --help' for help >> text. >> > >> >Nick >> > >> > >> >On Thu, 2005-09-01 at 17:06 +1000, Fornito, Alexander wrote: >> >> Hi, >> >> We've recently installed the >> freesurfer-Linux-rh9-dev20050729.tar.gz distribution along >> with fs_supportlibs.tar.gz. >> >> csurf works ok, but if i try to run tksurfer, I get the >> error message below. We'd appreciate any help as we've been >> stuck for a while. >> >> Thanks! >> >> >> >> tksurfer 1000027 rh white >> >> surfer: current subjects dir: >> /data/flanders/work/alex/freesurfer/subjects >> >> surfer: not in "scripts" dir ==> using cwd for session root >> >> surfer: session root data dir ($session) set to: >> >> surfer: /data/flanders/work/alex/freesurfer/subjects >> >> surfer: Reading header info from >> /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info >> >> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be >> found. >> >> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be >> found. >> >> surfer: vertices=152190, faces=304376 >> >> surfer: single buffered window >> >> Xlib: extension "XFree86-DRI" missing on display ":0.0". >> >> Tix_Init failed: version conflict for package "Tcl": have >> 8.3, need 8.4 >> >> surfer: using interface >> /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl >> >> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl >> >> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl >> >> Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl >> >> couldn't load file "/usr/lib/libtix8.1.8.4.so": >> /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No >> such file or directorysurfer: Error sending tcl command >> UpdateUndoItemLabel "Nothing to Undo": >> >> invalid command name "UpdateUndoItemLabel" >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: >> >> can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: >> >> can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: >> >> can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: >> >> can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: >> >> can't read "glMenuGroups(mg_TimeCourseLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: >> >> can't read "glMenuGroups(mg_OverlayLoaded)": no such variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: >> >> can't read "glMenuGroups(mg_CurvatureLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: >> >> can't read "glMenuGroups(mg_LabelLoaded)": no such variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: >> >> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> variable >> >> % surfer: Error sending tcl command MoveToolWindow 663 670: >> >> invalid command name "MoveToolWindow" >> >> surfer: Error sending tcl command MoveToolWindow 663 670: >> >> invalid command name "MoveToolWindow" >> >> surfer: Error sending tcl command MoveToolWindow 663 670: >> >> invalid command name "MoveToolWindow" >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >________________ >> >fs_lib_check (4k bytes) >> >> >

3 3

Fix_topology error
by Clifford A. Smith, PhD 02 Sep '05

02 Sep '05

Ran recon-all autorecon1 without a problem. Ran recon-all autorecon2 with the following error being produced with mris_fix_topology. Any suggestions on proceeding? Cliff Fix Topology rh Wed Aug 31 19:49:23 CDT 2005 /Users/Shared/freesurfer/subjects/00139/scripts mris_fix_topology -ga -mgz 00139 rh ************************************************************* Setting options using genetic algorithm with optimized parameters ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* reading input surface /Users/Shared/freesurfer/subjects/00139/surf/rh.qsphere... INFO: Volume /tmp/mritotal_10838/nu_8_dxyz.mnc cannot be found. before topology correction, eno=-116 (nv=134843, nf=269928, ne=404887, g=59) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 8916 ambiguous faces found in tessellation segmenting defects... 57 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 4 -merging segment 24 into 21 55 defects to be corrected 0 vertices coincident Computing Initial Surface Statistics -face loglikelihood: -8.5791 (-4.2896) -vertex loglikelihood: -5.5509 (-2.7754) -normal dot loglikelihood: -3.5429 (-3.5429) -quad curv loglikelihood: -6.4438 (-3.2219) Total Loglikelihood : -24.1167 CORRECTING DEFECT 0 Computing statistics for defect 0 [ (128,159,42) - 91.055 ] -white ( 95.29 , 2.78 ) -gray ( 85.38 , 4.30 ) -gray ( 89.45 , 18.92 ) - white ( 99.58 , 17.72 ) -intensity (85.375229 [log = -2.390182 ]- 95.286507 [log = -1.957521 ]) -curvature(kmax=-0.093632 : rmin = 10.680127 | kmin=-0.036819 : rmax = 27.159932 ) - k1 ( -0.06 , 0.70 ) - k2 ( -0.02 , 0.26 ) retessellating defect 0 with 55 vertices (convex hull=80). 125 of 1360 overlapping edges discarded Defect size : 16 by 15 by 13 (scale = 2) Edge Clustering: 3 segments were found (1 were discarded ) cluster 0 has 29 edges cluster 1 has 13 edges cluster 2 has 13 edges l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 new optimal fitness found at 4: -68.6645 Initial population for defect 0: best fitness at 4: -68.6645 (-70.9431 +- 2.5561) Segmentation fault recon-all exited with errors at Wed Aug 31 19:50:44 CDT 2005 ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

2 2

Re: [Freesurfer] Lib prob?
by xmeadow＠uchicago.edu 01 Sep '05

01 Sep '05

Hi, I downloaded what hopefully is the correct version of blt, and after that ran your script and said everything was fine in terms of libraries. However, I did have to create two soft links. The first one was a softlink from libtix8.1.8.3 to libtix8.1.8.4 in /usr/lib. The second was a softlink from tixwish8.1.8.3 to tixwish8.1.8.4 in /usr/bin. After making both of these changes I was able to run csurf, but when I tried to view an inflated brain the brain image would come up, but then freesurfer freezes and I can't do anything. In the logs I get the following errors: can't read "glMenuGroups(mg_FieldSignLoaded)": no such varialble surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable tksurfer: run tcl script: /tmp/TmpTclSurf.13311 Unfortunately these error messages mean nothing to me, so I was wondering if anyone else had seen them before. Thanks very much. >Xander ---- Original message ---- >Date: Thu, 01 Sep 2005 11:08:52 -0400 >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Lib prob? >To: xmeadow(a)uchicago.edu, "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au> >Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > >Alex and Xander, > >>From reading the error messages in your emails, it appears that >freesurfer is not able to find the tcl/tk, and tix libraries on your >platform. > >We have been working on trying to provide a seamless solution to the >problem of freesurfer finding the external libraries upon which it >depends, on the varied platforms that it supports. > >To help, later today, a new 'dev' build for rh9 that includes many of >the necessary libraries will be posted for download. This is not a >'stable' release (which is still undergoing testing), but a >'development' (dev) build, so it is still possible to have installation >problems, but hopefully it will install and work for you. I will email >you again when it is ready, and your patience is appreciated. > >In the meantime, I've attached a script, called 'fs_lib_check', which >will check your system for the libraries that freesurfer requires. I'm >curious to know the results of its output for your systems. Just type >'fs_lib_check' to run it, and 'fs_lib_check --help' for help text. > >Nick > > >On Thu, 2005-09-01 at 17:06 +1000, Fornito, Alexander wrote: >> Hi, >> We've recently installed the freesurfer-Linux-rh9-dev20050729.tar.gz distribution along with fs_supportlibs.tar.gz. >> csurf works ok, but if i try to run tksurfer, I get the error message below. We'd appreciate any help as we've been stuck for a while. >> Thanks! >> >> tksurfer 1000027 rh white >> surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects >> surfer: not in "scripts" dir ==> using cwd for session root >> surfer: session root data dir ($session) set to: >> surfer: /data/flanders/work/alex/freesurfer/subjects >> surfer: Reading header info from /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info >> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. >> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. >> surfer: vertices=152190, faces=304376 >> surfer: single buffered window >> Xlib: extension "XFree86-DRI" missing on display ":0.0". >> Tix_Init failed: version conflict for package "Tcl": have 8.3, need 8.4 >> surfer: using interface /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl >> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl >> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl >> Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl >> couldn't load file "/usr/lib/libtix8.1.8.4.so": /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No such file or directorysurfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": >> invalid command name "UpdateUndoItemLabel" >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: >> can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: >> can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: >> can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: >> can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: >> can't read "glMenuGroups(mg_TimeCourseLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: >> can't read "glMenuGroups(mg_OverlayLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: >> can't read "glMenuGroups(mg_CurvatureLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: >> can't read "glMenuGroups(mg_LabelLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: >> can't read "glMenuGroups(mg_FieldSignLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable >> % surfer: Error sending tcl command MoveToolWindow 663 670: >> invalid command name "MoveToolWindow" >> surfer: Error sending tcl command MoveToolWindow 663 670: >> invalid command name "MoveToolWindow" >> surfer: Error sending tcl command MoveToolWindow 663 670: >> invalid command name "MoveToolWindow" >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >________________ >fs_lib_check (4k bytes)

2 2

mri_convert with *.IMG
by Michele Perry 01 Sep '05

01 Sep '05

Hi, I was given some MRI structural data originally scanned on a GE Signa 5. It was converted from Genesis to 8-bit *.tif's and 16-bit *.IMG's (with corresponding *.HDR files). The raw data is 256 pixels x 256 pixels x 2 bytes, little endian Intel. There are 124 .TIF, .IMG and .HDR files I have tried to convert from .IMG to COR using mri_convert -it <see below> -ot cor /path/001.IMG $SUBJECTS_DIR/subjid/mri/orig Here's what I get... -it anaylze -ot cor (I get errors if I don't give an output type) (result: reading from /path/001.IMG... analyzeRead(): cannot find any files for /path/001.IMG) -it ge -ot cor (result: reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG) -it gelx -ot cor reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG I have tried running this with the .IMG files in their own separate directory and in a directory with the .HDRs and .TIFs. I've also tried running it without specifing the .IMG file, just the directory. Any ideas what I'm doing wrong? Michele

1 0

Mac OS Server and X11 forwarding
by Yuan-Fen Kuo 01 Sep '05

01 Sep '05

Hi: We have installed the Tiger distribution on our Xserve. When we SSH with X forwarding on, and run tkmedit with our Mac laptops and linux stations, we get GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by display: localhost:13.0 We could only successfully launch tkmedit if we log in from a Sun station. Any suggestions is appreciated. Thanks, Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison

2 2

flattening full patch
by Don Hagler 01 Sep '05

01 Sep '05

When I try to do a full flattening of a surface I often get areas with extreme squishing, looking like wrinkles. Usually if I redo the cuts in slightly different ways (e.g. adjust the spacing between cuts, extend the cuts farther onto the lateral surface, etc) I can get the flattened surface to come out looking smooth. Sometimes it takes several attempts (with several hours of computation for each attempt) to get it right. Has anyone else noticed this, and has anyone attempted to improve the flattening algorithm?

1 0

Lib prob?
by Fornito, Alexander 01 Sep '05

01 Sep '05

Hi, We've recently installed the freesurfer-Linux-rh9-dev20050729.tar.gz distribution along with fs_supportlibs.tar.gz. csurf works ok, but if i try to run tksurfer, I get the error message below. We'd appreciate any help as we've been stuck for a while. Thanks! tksurfer 1000027 rh white surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/flanders/work/alex/freesurfer/subjects surfer: Reading header info from /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. surfer: vertices=152190, faces=304376 surfer: single buffered window Xlib: extension "XFree86-DRI" missing on display ":0.0". Tix_Init failed: version conflict for package "Tcl": have 8.3, need 8.4 surfer: using interface /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl couldn't load file "/usr/lib/libtix8.1.8.4.so": /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No such file or directorysurfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": invalid command name "UpdateUndoItemLabel" surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: can't read "glMenuGroups(mg_TimeCourseLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: can't read "glMenuGroups(mg_OverlayLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: can't read "glMenuGroups(mg_CurvatureLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: can't read "glMenuGroups(mg_LabelLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: can't read "glMenuGroups(mg_FieldSignLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable % surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow"

3 2

global thickness
by Goldman, Aaron (NIH/NIMH) 01 Sep '05

01 Sep '05

Hi, For each of my subjects, I'd like to obtain a global value of their average thickness. What would be the best way to do this? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov <mailto:aarong@mail.nih.gov>

3 2

documentation of matrix format for talairach transform
by Tracy Wang 31 Aug '05

31 Aug '05

Hi all, I was wondering if anyone knows what the format of the matrix in the talairach.xfm file is or if there is any documentation available describing the matrix format. Thanks! Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

3 2

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