Dear all,<div><br></div><div>After moving my data to a different folder, I&#39;ve come across a different error when running recon-all (autorecon2 and 3).  The last few lines are as follows:</div><div><br></div><div><div>0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766</div>

<div>0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766</div><div>0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766</div><div>0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766</div><div>0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766</div>

<div>Killed</div><div>ERROR: mri_ca_register with non-zero status 137</div><div>but continuing despite the error</div><div>#--------------------------------------</div><div>#@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012</div>

<div>/home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri</div><div><br></div><div> mri_ca_register -invert-and-save transforms/talairach.m3z </div><div><br></div><div>Loading, Inverting, Saving, Exiting ...</div>
<div>
Reading transforms/talairach.m3z </div><div>ERROR: cannot find or read transforms/talairach.m3z</div><div>ERROR: mri_ca_register with non-zero status 0</div><div>Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux</div>

<div><br></div><div>recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012</div></div><div><br></div><div><br></div><div>Another set is exiting simply with:</div><div><br></div><div><div>#@# EM Registration Mon Nov 12 17:43:05 HKT 2012</div>

<div>/home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri</div><div><br></div><div> mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta </div>

<div><br></div><div>Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux</div><div><br></div><div>recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012</div><div>

<br></div><div>To report a problem, see <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting">http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting</a></div></div><div><br></div><div><br></div><div><br></div><div>

What&#39;s the problem I should be addressing?</div><div><br></div><div>Thanks!</div><div><br></div><div>Cheers,</div><div>Linda</div><div><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 2 November 2012 21:40, Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu" target="_blank">fischl@nmr.mgh.harvard.edu</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Linda<br>
<br>
it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else<br>
<br>
cheers<br>
Bruce<div><div class="h5"><br>
<br>
<br>
On Fri, 2 Nov 2012, Linda Zhang wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all,<br>
I&#39;ve been running recon-all on my dataset, but all of them are exiting with<br>
the same error.  <br>
<br>
The command line is:<br>
recon-all -subjid ncpoCCW -autorecon2 -autorecon3<br>
<br>
The error reads:<br>
#@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012<br>
INFO: lh.EC_average subject does not exist in SUBJECTS_DIR<br>
INFO: Creating symlink to lh.EC_average subject...<br>
<br>
 cd /home/virtualuser/freesurfer/<u></u>subjects; ln -s<br>
/home/virtualuser/freesurfer/<u></u>subjects/lh.EC_average; cd - <br>
<br>
<br>
 mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label<br>
lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label <br>
<br>
painting output onto subject ncpoCCW.<br>
processing subject lh.EC_average...<br>
MRISread(/home/virtualuser/<u></u>freesurfer/subjects/lh.EC_<u></u>average/surf/lh.sphere<br>
.reg): could not open file<br>
eroding label 1 times before writing<br>
thresholding label stat at 0.400 before writing<br>
Too many levels of symbolic links<br>
mris_spherical_average: could not read surface file<br>
/home/virtualuser/freesurfer/<u></u>subjects/lh.EC_average/surf/<u></u>lh.sphere.reg<br>
Too many levels of symbolic links<br>
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC<br>
2011 i686 GNU/Linux<br>
<br>
recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012<br>
<br>
What should I do?  Thanks!<br>
<br>
Cheers,<br>
Linda<br>
<br>
<br>
</blockquote>
<br>
<br></div></div>
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