Mithra,

Confirm that your skull-stripped volume (brainmask.mgz) shows just brain w/o skull, and that is has the cerebellum intact.

You could also send me the brainmask.mgz and nu.mgz files, and i can have a look. If you want to do that, use the filedrop to upload those files to me:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick

On Tue, 2006-10-31 at 14:47 -0600, Mithra wrote:

Hello,

I ran autorecon1 this step worked fine. The transform obtained from this step looked good.

When I run autorecon2, I get a segmentation fault error.

Can anybody tell me whats wrong.

Thanks a whole bunch.

Error:

Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux WM removal version #------------------------------------- #@# EM Registration Tue Oct 31 14:32:46 CST 2006 /usr/pubsw/freesurfer/subjects/sub02/mri

mri_em_register -mask brainmask.mgz nu.mgz /usr/pubsw/freesurfer/average/RB_all _2006-02-15.gca transforms/talairach.lta

using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/pubsw/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Tue Oct 31 14:32:57 CST 2006

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