try running the mri_remove_neck command line manually. If that doesn't work try changing the nu_neck.mgz name to nu_noneck.mgh and running gzip on it
On Tue, 30 May 2006, Graham Wideman wrote:
At 5/30/2006 01:38 PM, Doug Greve wrote:
I've put a new Linux version of mri_remove_neck at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_remove_neck Can you run this? It prints more info about why it's failing. doug
Thanks Doug... here are the results, and it looks like Bruce's guess was in the right area :-)
I ran:
recon-all -autorecon2 -nogcareg -nocanorm -nocareg -nocareginv
... so as to run only the Remove Neck step, and here's what I get:
#-------------------------------------- #@# Remove Neck Tue May 30 13:56:46 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c > nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 30 14:08:38 PDT 2006
Any ideas on this? I've not sure which program is issuing which error.
Graham
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