Hi Cyrus,

it's almost certainly running out of ram. How much do you have in that machine/VirtualBox?

Bruce

On Wed, 9 May 2012, Sarosh, Cyrus wrote:

I have run recon?all on multiple subjects and have had it fail at the same step every time with the same error. I am using VirtualBox with the provided Disk Image and Windows 7.

0560: dt=0.001750, rms=0.358 (0.039%), neg=0, invalid=766

GCAMwrite(transforms/talairach.m3z): gzip encountered error.

writing output transformation to transforms/talairach.m3z...

GCAMwrite

GCAMwrite:: m3z loop

GCAMwrite:: the command is:  gzip -f -c > transforms/talairach.m3z

GCAMwrite:: the popen error code is:  12

mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed

ERROR: mri_ca_register with non-zero status 252

but continuing despite the error

#--------------------------------------

#@# CA Reg Inv Tue May  8 16:45:14 EDT 2012

/home/virtualuser/freesurfer/subjects/test/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 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

recon-all -s test exited with ERRORS at Tue May  8 16:45:15 EDT 2012

Has anyone had this issue and resolved this problem? Thanks for your help.

-          Cyrus

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