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
#@# 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. #-------------------------------------- #@# 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
Please send the entire log file.
sbasho@nmr.mgh.harvard.edu 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
#@# 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. #-------------------------------------- #@# 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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-
Doug Greve -
sbasho＠nmr.mgh.harvard.edu