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.
#--------------------------------------
[EMAIL PROTECTED] 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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