Nick,

Here's the output:

[derin@eeyore conte_mprage]$ ldd `which tkmedit.bin` linux-gate.so.1 => (0x00590000) libtix8.1.8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so (0x001c3000) libtk8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0x00e8b000) libtcl8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x006c6000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00110000) libGL.so.1 => /usr/lib/libGL.so.1 (0x06531000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0088e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x00789000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0x00223000) libz.so.1 => /usr/lib/libz.so.1 (0x0067b000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x0713a000) libdl.so.2 => /lib/libdl.so.2 (0x0065c000) libpthread.so.0 => /lib/libpthread.so.0 (0x00662000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x07680000) libm.so.6 => /lib/libm.so.6 (0x00633000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0763a000) libc.so.6 => /lib/libc.so.6 (0x0023a000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0x056f8000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0x00190000) libXau.so.6 => /usr/lib/libXau.so.6 (0x0077c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00781000) libXt.so.6 => /usr/lib/libXt.so.6 (0x06e01000) /lib/ld-linux.so.2 (0x004cb000) libSM.so.6 => /usr/lib/libSM.so.6 (0x00438000) libICE.so.6 => /usr/lib/libICE.so.6 (0x0045f000)

[derin@eeyore conte_mprage]$ ldd `which tksurfer.bin` linux-gate.so.1 => (0x00f6e000) libtix8.1.8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so (0x002e6000) libtk8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0x003ce000) libtcl8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x00110000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0x006f7000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0x00223000) libGL.so.1 => /usr/lib/libGL.so.1 (0x06531000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0088e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x00789000) libz.so.1 => /usr/lib/libz.so.1 (0x0067b000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x0713a000) libdl.so.2 => /lib/libdl.so.2 (0x0065c000) libpthread.so.0 => /lib/libpthread.so.0 (0x00662000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x07680000) libm.so.6 => /lib/libm.so.6 (0x00633000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0763a000) libc.so.6 => /lib/libc.so.6 (0x004ee000) libXt.so.6 => /usr/lib/libXt.so.6 (0x06e01000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0x056f8000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0x00259000) libXau.so.6 => /usr/lib/libXau.so.6 (0x0077c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00781000) /lib/ld-linux.so.2 (0x004cb000) libSM.so.6 => /usr/lib/libSM.so.6 (0x001ad000) libICE.so.6 => /usr/lib/libICE.so.6 (0x001b6000)

For our network: $FREESURFER_HOME=/pkg/brainmap/freesurfer

Thanks,

Derin

On Oct 9, 2008, at 3:40 PM, Nick Schmansky wrote:

Derin,

Can you do this:

source $FREESURFER_HOME/bin/tcl_setup

then send me the output of:

ldd `which tkmedit.bin`

and

ldd `which tksurfer.bin`

I will be looking to see if the proper tcl/tk/tix/blt libs are being used (those in freesurfer/lib/tcltktixblt).

Nick

On Thu, 2008-10-09 at 11:15 -0500, Derin Cobia wrote: Nick,

Yes, our tcltktixblt directory was intact and set correctly. The reason I thought it was a BLT lib was it came up missing when I ran fs_lib check. At any rate, the DefaultDepth is already at 24 in our xorg.conf file and the problem persists. Any other thoughts what might be occurring? Would you like me to submit my output as well?

Also, any thoughts from anyone with regard to question #2 (see below)? Thanks.

-Derin

On Oct 8, 2008, at 5:12 PM, Nick Schmansky wrote:

Derin,

To answer your first question, the solution to that particular problem that you reference was not to install the BLT libs (as they are included with freesurfer in the $FREESURFER_HOME/lib/tcltktixblt directory and found by setting LD_LIBRARY_PATH in the tksurfer script), but rather by changing the 'DefaultDepth' from 16 to 24 in the 'Screen' Section in the file /etc/X11/xorg.conf file.

Nick

Two questions:

1. We installed the latest version of 32-bit FS on several workstations running CentOS 5.1 in our lab. However, once we ran the CentOS updates (~280 of them through up2date), tkmedit now fails to open and tksurfer exhibits behavior exactly as described in this message from the mail archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html Having attempted to troubleshoot it I discovered that a blt lib was missing, but even with re-installation of this tksurfer continues to not display correctly. I believe it's a tcl problem, but I don't understand why performing incremental updates to CentOS would break FS. More importantly, I'm not sure which of the updates does "the breaking" so I can just avoid it. Any ideas?

2. We are in the process of training new research assistants in how to use FS. Typically we have approached this in a more qualitative way by working side-by-side with them to guide their edits and processing. I was wondering if there is a quantitative way of comparing their work that you (or others) have used when training "new recruits" in FS. Maybe something like was done in the Han et al (2006) paper, such as compare their thickness (or other) maps with someone we know does well with manual interventions? In essence, we're trying to think of a rigorous way to train new people in FS, thanks!

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