Tracy Wang wrote:
Hi all, I'm trying to run tkregister2 and I have the following questions:
- 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. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.tar.gz
- 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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