Dear Nick,
I tried the newest centos4 build (20060223) but to no avail. I still cannot see bert's entire pial surface using the command
tksurfer bert rh pial
Do you have further suggestions? Do you know of someone using freesurfer under debian "etch"?
Marcus
Nick Schmansky wrote:
Marcus,
You may want to try the centos4 build of freesurfer. It is built against libstdc++.so.6, whereas the rh9 build builds against libstdc+ +.so.5.
I don't know whether this would account for the partial brain you are seeing, or why, but its worth a try.
Nick
On Wed, 2006-02-22 at 10:58 +0100, wilms wrote:
Dear all,
does someone out there run freesurfer (freesurfer-Linux-rh9-dev20060210-full.tar.gz) under debian etch? Installation runs smoothly, however, when I test the freesurfer installation with
medpc32:~$ tksurfer bert rh pial
only a tiny fraction of Bert's brain is displayed. The GUI otherwise seems to work as I can rotate etc this brain fraction.
I installed the same freesurfer version on a different computer running debian "sarge", which is the current stable distribution. - Here, I can see the whole brain!
As suggested elsewhere I thus compared the shared library dependencies using
medpc32:~$ ldd `which tkmedit`
Here is what I got:
######### "etch"-machine: #########
medpc32:~$ ldd `which tkmedit` linux-gate.so.1 => (0xffffe000) libtix8.1.8.3.so => /local/opt/freesurfer_dev20060210/lib/tcltktixblt/lib/libtix8.1.8.3.so (0xb7fb0000) libtk8.4.so => /local/opt/freesurfer_dev20060210/lib/tcltktixblt/lib/libtk8.4.so (0xb7ef0000) libtcl8.4.so => /local/opt/freesurfer_dev20060210/lib/tcltktixblt/lib/libtcl8.4.so (0xb7e57000) libglut.so.3 => /usr/lib/libglut.so.3 (0xb7e0d000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0xb7e04000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0xb7dec000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0xb7dd6000) libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0xb7dce000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7d4f000) libGL.so.1 => /usr/lib/libGL.so.1 (0xb7ceb000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0xb7c20000) libgsl.so.0 => /local/opt/freesurfer_dev20060210/lib/gsl/lib/libgsl.so.0 (0xb7acc000) libgslcblas.so.0 => /local/opt/freesurfer_dev20060210/lib/gsl/lib/libgslcblas.so.0 (0xb7a9c000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb7a7c000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0xb7a2a000) libz.so.1 => /usr/lib/libz.so.1 (0xb7a15000) libm.so.6 => /lib/tls/libm.so.6 (0xb79ef000) libcrypt.so.1 => /lib/tls/libcrypt.so.1 (0xb79c1000) libc.so.6 => /lib/tls/libc.so.6 (0xb788a000) libdl.so.2 => /lib/tls/libdl.so.2 (0xb7886000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0xb7878000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0xb7827000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb774a000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb773f000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0xb772d000) libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0xb7728000) /lib/ld-linux.so.2 (0xb7feb000)
######### "sarge" machine: #########
kogneuro-web:~$ ldd `which tkmedit` libtix8.1.8.3.so => /local/data/tools/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0xb7fae000) libtk8.4.so => /local/data/tools/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0xb7eee000) libtcl8.4.so => /local/data/tools/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0xb7e55000) libglut.so.3 => /usr/lib/libglut.so.3 (0xb7e1b000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0xb7e12000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0xb7dfb000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0xb7de4000) libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0xb7ddc000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7d61000) libGL.so.1 => /usr/lib/libGL.so.1 (0xb7cf2000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0xb7c2b000) libgsl.so.0 => /local/data/tools/freesurfer/lib/gsl/lib/libgsl.so.0 (0xb7ad7000) libgslcblas.so.0 => /local/data/tools/freesurfer/lib/gsl/lib/libgslcblas.so.0 (0xb7aa6000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb7a88000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0xb7a38000) libz.so.1 => /usr/lib/libz.so.1 (0xb7a26000) libm.so.6 => /lib/tls/libm.so.6 (0xb7a04000) libcrypt.so.1 => /lib/tls/libcrypt.so.1 (0xb79d7000) libc.so.6 => /lib/tls/libc.so.6 (0xb78a1000) libdl.so.2 => /lib/tls/libdl.so.2 (0xb789e000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0xb7890000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0xb783f000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xb7785000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7779000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0xb776a000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0xb7fea000)
The differences seem to be:
######### "etch" machine: ######### libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb774a000) libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0xb7728000) /lib/ld-linux.so.2 (0xb7feb000)
######### "sarge" machine: ######### libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xb7785000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0xb7fea000)
Does this mean that the c++ libraries on my etch-running machine are "too" new? Why is there no "=>" for /lib/ld-linux.so.2 on my etch-running machine?
I would greatly appreciate any comments or ideas what else I could do.
Many thanks in advance,
Marcus