I also checked without the '--surf orig'. Still not found.
On 8 March 2010 14:22, Janani Dhinakaran janinthesky@gmail.com wrote:
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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- I am the Sun, I know no darkness.