Please send the entire log file.
[EMAIL PROTECTED] wrote:
Hello,
I received an error when running recon-all. It seems to have run into a
problem during the 'Remove Neck' and 'SkullLTA' steps. I have included
the output below of the last two steps before the error occured. Thank
you.
-Surina
[EMAIL PROTECTED] Remove Neck Wed Jul 19 15:26:17 EDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z
/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain
reading atlas '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'...
setting gca type = Normal gca type
reading input volume 'nu.mgz'...
reading transform 'transforms/talairach.m3z'...
mghWrite(nu_noneck.mgz, -1): could not open file
gcam->type = vox
reading labels out of gcam file...
removing structures at least 25 mm from brain...
11405488 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 23 minutes and 41 seconds.
#--------------------------------------
[EMAIL PROTECTED] SkullLTA Wed Jul 19 15:50:02 EDT 2006
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz
/usr/local/freesurfer/stable/average/RB_all_withskull_2006-02-15.gca
transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach_with_skull.log
reading
'/usr/local/freesurfer/stable/average/RB_all_withskull_2006-02-15.gca'...
setting gca type = Normal gca type
average std = 23.5 using min determinant for regularization = 55.2
0 singular and 6473 ill-conditioned covariance matrices regularized
reading 'nu_noneck.mgz'...
zcat:
/autofs/space/tango_003/users/recon_modygp/surina/mody096/mri/nu_noneck.mgz.gz:
No such file or directory
mghRead(/autofs/space/tango_003/users/recon_modygp/surina/mody096/mri/nu_noneck.mgz,
-1): read error
mri_em_register: could not open input volume nu_noneck.mgz.
Linux whump 2.6.9-34.ELsmp #1 SMP Wed Mar 8 00:27:03 CST 2006 i686 i686
i386 GNU/Linux
recon-all exited with ERRORS at Wed Jul 19 15:50:30 EDT 2006
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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