what version are you using? I actually thought MRI_DIR was deprecated. Try doing:

setenv MRI_DIR $FREESURFER_HOME

and see if that fixes it.

cheers Bruce

I actually t On Thu, 9 Sep 2010, ckung wrote:

Dear all:

I installed Freesurfer, tested it with the recommended commands listed in

http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer

and encountered a problem only in tksurfer. When I hit

tksurfer yc (or bert) lh pial

I get two kinds of error messages:

can't find talairach file '/Volumes/Sophomore/ncku_KMU_fMRI/surfaces/yc/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: single buffered window surfer: tkoInitWindow(yc) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.new.tcl Error sourcing /Applications/freesurfer/lib/tcl/tksurfer.new.tcl: can't read "env(MRI_DIR)": no such variable

I found both problems have been asked before (one at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02372.html another http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00029.html

and I tried to mimic the solution provided, but no luck so far. The problem persists. So I wonder if gurus in this forum might be kind enough to suggest some directions? I was baffled by this "small" problems for almost 1 week, so....

many thanks, chun-chia

p.s., I checked the .xdebug_tksurfer returned empty files, and I am not sure where is the log file located...