check the brainmask.mgz to see if it looks reasonable On Thu, 30 Nov 2006, Bum Seok Jeong wrote:

I'm trying to analyze 3T spgr image with freesurfer. I faced error message during autorecon2 step. And typed 'recon-all -autorecon2 -conorm -subjid case**** to figure out which process it occured in.

This is error message after putting '-conorm' tag.

..... registration took 7 minutes and 3 seconds. #-------------------------------------- #@# CA Normalize Thu Nov 30 11:12:00 EST 2006 /gr/caseD00916/mri

mri_ca_normalize -mask brainmask.mgz nu.mgz /freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz

using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... GCAhistoScaleImageIntensities: could not find wm peak reading input volume from nu.mgz... resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=39.0 using (126, 155, 152) as brain centroid... mean wm in atlas = 116, using box (126,155,136) --> (125, 154,168) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Linux 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Thu Nov 30 11:12:16 EST 2006

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