Hi Christine,
usually this means it is running out of memory. I think we recommend more than 2G for a virtual machine, can you increase the amount of RAM?
cheers Bruce On Mon, 26 Jul 2010, MacDonald, Christine wrote:
Greetings from St. Louis. I recently installed Freesurfer version 4.5 on my Windows XP OS PC after attending your training course held at our institution, Washington University. The install went fine, and I was able to make it through all the checks in your setup and installation series on your wiki page. I attempted to then run a data set of my own and ran into the following error during autorecon2 which I have included the lines of output right before it as well:
setting smoothness coefficient to 2.00
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.465, neg=0, invalid=766
0495: dt=0.028000, rms=0.464 (0.163%), neg=0, invalid=766
0496: dt=0.028000, rms=0.463 (0.154%), neg=0, invalid=766
0497: dt=0.024000, rms=0.463 (0.124%), neg=0, invalid=766
0498: dt=0.000438, rms=0.463 (0.002%), neg=0, invalid=766
0499: dt=0.000438, rms=0.463 (0.002%), neg=0, invalid=766
0500: dt=0.000219, rms=0.463 (0.001%), neg=0, invalid=766
0501: dt=0.000014, rms=0.463 (0.000%), neg=0, invalid=766
0502: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=766
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.463, neg=0, invalid=766
0503: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=766
Segmentation fault
ERROR: mri_ca_register with non-zero status 139
but continuing despite the error
#--------------------------------------
#@# CA Reg Inv Fri Jul 23 18:12:09 EDT 2010
/data/TB3241W/TB3241W/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
recon-all exited with ERRORS at Fri Jul 23 18:12:10 EDT 2010
I am running with 4G of RAM and a quad-core processor. At first I thought it was because of the 2GB max space limit in VMware so I even built and mounted a 100GB drive internal to VMware and ran all the data from there. Additionally when I check the disk space after this error it shows it only used ~1% of the 100GB mounted disk in VMware so I know I have room. Output from typing 'bugr' per your request on wiki is the following:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0
Debian version: 5.0
Kernel info: Linux 2.6.28-11-generic i686
Any thoughts or guidance as to what may be going wrong? I fully admit to my novice status with Freesufer and kindly look forward to any and all advice. I found one reference to a similar problem searching through your Freesurfer support Old Archive but the response from your organization was just a further inquiry for additional information so I was unsure as to how to proceed. Thank you in advance for the help!
Best Regards,
Christine Mac Donald
Washington University
Saint Louis, MO