Hi Doug,
thanks for answering so quickly. Actually i ran recon-all -subjid 000112_vc1552_test -autorecon1 which i think would include the initial talairaching stage correct?

the talairach tranform seemed problematic both when viewed in tkmedit and the final objective funtion value in the mritotal.log (ours was 0.15870732).

does this mean that the talairaching failed at some place? How can i tell because mritotal seems to run to completion?

Thanks again,
Tracy


On Jul 28, 2005, at 4:52 PM, Doug Greve wrote:

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?

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.tar.gz.



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

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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422