Here is how I checked if it was done okay
Looks like it wasn't.

s0964091@CRIC-0012:~$ export SUBJECTS_DIR=~/Desktop/Newdata
s0964091@CRIC-0012:~$ tkregister2 --mgz --s tal_before --fstal --surf orig
tkregister_tcl /usr/local/freesurfer/lib/tcl/tkregister2.tcl
surfname set to orig
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume (null)
reg file       (null)
LoadVol        1
ZeroCRAS       1
$Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $
Diagnostic Level -1


WARNING: cannot write to /home/s0964091/Desktop/Newdata/tal_before/mri/transforms.
You will not be able to save any edits.
Hit Enter to continue:
 ... continuing

regio_read_mincxfm: No such file or directory
ERROR: could not read /home/s0964091/Desktop/Newdata/tal_before/mri/transforms/talairach.xfm

On 8 March 2010 14:09, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

That is a message from the routine that we use to automatically check the tal transform. Sometimes it is too conservative. You should check the transform manually with tkregister2. If it looks ok, then you can run recon-all with -notal-check. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach for more info.

doug

Janani Dhinakaran wrote:

Any idea what this means and what I can do about it?

Mon Mar  8 12:46:58 GMT 2010
talairach_avi done
#--------------------------------------------
#@# Talairach Failure Detection Mon Mar  8 12:46:58 GMT 2010
/home/s0964091/Desktop/Newdata/JS/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Linux CRIC-0012 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux

recon-all exited with ERRORS at Mon Mar  8 12:46:58 GMT 2010

Thank you
Jan
--
I am the Sun, I know no darkness.

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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I am the Sun, I know no darkness.