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:


<excerpt> Tracy Wang wrote:Hi all,

<excerpt> 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?


</excerpt>

<color><param>0000,0000,EEEE</param>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.tar.gz.</color>




 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

<excerpt>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

<color><param>0000,0000,EEEE</param>twang@artsci.wustl.edu</color> 

<fixed>

_______________________________________________

Freesurfer mailing list

<color><param>0000,0000,EEEE</param>Freesurfer@nmr.mgh.harvard.edu</color>

<color><param>0000,0000,EEEE</param>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</color></fixed>

</excerpt>


<fixed>-- 

Douglas N. Greve, Ph.D.

MGH-NMR Center

<color><param>0000,0000,EEEE</param>greve@nmr.mgh.harvard.edu</color>

Phone Number: 617-724-2358 

Fax: 617-726-7422

</fixed>


</excerpt><fontfamily><param>Courier</param><x-tad-bigger>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

</x-tad-bigger><color><param>9999,0000,0000</param><x-tad-bigger>twang@artsci.wustl.edu</x-tad-bigger></color><x-tad-bigger>

</x-tad-bigger></fontfamily>