Here is how I checked if it was done okay Looks like it wasn't. s0964...@cric-0012:~$ export SUBJECTS_DIR=~/Desktop/Newdata s0964...@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 <gr...@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. >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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.
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