Paul,

I've posted a build of freesurfer v4.1.0 that doesnt have this libexpat dependency. You can get it here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64

The alternative is to install the libexpat package via rpms or source.

Nick

On Fri, 2008-11-28 at 18:52 -0800, Paul Greenberg wrote:

Hello,

I am trying to run freesurfer on Ubuntu and recon-all fails to finish on the "bert" data set. Here is the output of bugr: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 Debian version: lenny/sid Kernel info: Linux 2.6.24-19-generic x86_64

I have already made a symbolic link to libtiff.so.3 based on previous archive messages using: "ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3"

Command Line: recon-all -all -subjid bert New error message: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance bert

mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory

After looking through some of the new archive posts on similar issues I typed: ldd /usr/local/freesurfer/bin/mris_volmask.bin and received the following output: linux-vdso.so.1 => (0x00007fff4e5fe000) libX11.so.6 => /usr/lib64/libX11.so.6 (0x00007fa045fcf000) libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x00007fa045db6000) libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00007fa045b37000) libvtkpng.so.5.2 => not found libvtksqlite.so.5.2 => not found libvtkzlib.so.5.2 => not found libexpat.so.0 => not found libvtkmetaio.so.5.2 => not found libvtkverdict.so.vtk5.2.0 => not found libvtkHybrid.so.5.2 => not found libvtkRendering.so.5.2 => not found libvtkGraphics.so.5.2 => not found libvtkImaging.so.5.2 => not found libvtkftgl.so.5.2 => not found libvtkIO.so.5.2 => not found libvtkFiltering.so.5.2 => not found libvtkCommon.so.5.2 => not found libvtkDICOMParser.so.5.2 => not found libvtksys.so.5.2 => not found libvtkexoIIc.so.5.2 => not found libvtkNetCDF.so.5.2 => not found libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00007fa045914000) libtiff.so.3 => /usr/lib64/libtiff.so.3 (0x00007fa0456bb000) libz.so.1 => /usr/lib64/libz.so.1 (0x00007fa0454a4000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00007fa04526c000) libdl.so.2 => /lib/libdl.so.2 (0x00007fa045068000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007fa044e4c000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fa044b41000) libm.so.6 => /lib/libm.so.6 (0x00007fa0448c0000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fa0446b2000) libc.so.6 => /lib/libc.so.6 (0x00007fa044350000) libxcb-xlib.so.0 => /usr/lib64/libxcb-xlib.so.0 (0x00007fa04414f000) libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00007fa043f34000) libXt.so.6 => /usr/lib64/libXt.so.6 (0x00007fa043cd0000) libSM.so.6 => /usr/lib64/libSM.so.6 (0x00007fa043ac8000) libICE.so.6 => /usr/lib64/libICE.so.6 (0x00007fa0438ad000) libXext.so.6 => /usr/lib64/libXext.so.6 (0x00007fa04369c000) /lib64/ld-linux-x86-64.so.2 (0x00007fa0462d2000) libXau.so.6 => /usr/lib64/libXau.so.6 (0x00007fa04349a000) libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00007fa043295000)

I'm not sure what the next step is, and thanks in advance for your help!

Paul

-- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg@ucsd.edu