Tracy Wang wrote:

Hi all,
I'm trying to run tkregister2 and I have the following questions:

1. It seems to look for a talairach directory in the main subject directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform?

It's looking for our talairach subject. I think this is part of the distribution, but if you don't have one, I've put a copy here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.tar.gz.

2. when tkregister tries to initialize, it tries to read the talairach.xfm file, but it's not finding the talairach.xform. What

does this mean? Here is the error output:

It means that you did not run the initial talairaching stage (eg, recon-all -talairach). If you don't want to run this first, you can run tkregister2 with --regheader (but be careful to run subsequent calls to recon-all with -notalairach to keep from overwriting). Also note that you can get help with tkregister2 --help

doug

tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig
surfname set to orig
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume (null)
reg file (null)
LoadVol 1
$Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $
Diagnostic Level -1
talairach.xfm ---------------------
0.874 -0.173 -0.004 -3.334;
0.188 0.957 -0.284 -10.880;
0.046 0.217 0.760 31.928;
0.000 0.000 0.000 1.000;
WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri
corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info
ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0

Thanks for any assistance!

Tracy Wang
Research Assistant
Cognitive Neuroscience Laboratory

Washington University
Department of Psychology, Campus Box 1125
One Brookings Drive
St. Louis MO 63130-4899
314-935-5019
twang@artsci.wustl.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422