error testing freesurfer installation - Freesurfer

28 Feb 2007


      Hi,
I just installed the rh9 version of fressurfer.
I am running Ubuntu 6.10.
I had the libtiff.so.3 error, which I seemed to have fixed by just making
a sym link to libtiff.so.4 ( I hope that is okay).
Now I get this error about the aseg.mgz.gz not existing. It looks like it
isn't looking in the mri/ dir as it should be.
mishkin@thinkpad:/usr/local/freesurfer$ tkmedit bert norm.mgz
-segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
libGL warning: 3D driver claims to not support visual 0x5b
  Talairach transform
/autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does
not exist ...
Loading tal xfm file
/usr/local/freesurfer/subjects/bert/mri/transforms/talairach.xfm
zcat: /usr/local/freesurfer/subjects/bert//aseg.mgz.gz: No such file or
directory
mghRead(/usr/local/freesurfer/subjects/bert//aseg.mgz, -1): read error
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
These are the only things i've added to my .bashrc :
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
which produces this output:
-------- freesurfer-Linux-rh9-stable-pub-v3.0.5 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME     /usr/local/freesurfer/fsfast
SUBJECTS_DIR    /usr/local/freesurfer/subjects
MNI_DIR         /usr/local/freesurfer/mni
GSL_DIR         /usr/local/freesurfer/lib/gsl
FSL_DIR         /usr/local/freesurfer/fsl
Did I forget to set a variable somewhere?
thanks,
mishkin