Tom,
brain.mgz is not produced by the -autorecon1 stage, rather, it is
produced by the autorecon2 stage. for reference, see:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
brain.mgz should have been updated during the second normalization step
(-normalization2). consult the subjects scripts/recon-all.log for a
play-by-play. what aspect of the autorecon2 output was horrendous?
Nick
On Tue, 2006-03-28 at 15:30 -0500, Tom Bayer wrote:
After running "recon-all -autorecon1" I saw that brain.mgz was missing
some large areas in the cerebellum.
I ran "recon-all -skullstrip -wsthreshold 35" and then checked my work
with "tkmedit subjid brainmask.auto.mgz -aux T1.mgz"
The skullstrip looked very good, so I went on to run autorecon2.
brain.mgz was never updated and the output of autorecon2 was
horrendous.
I am going to use mri_mask to generate a new brain.mgz using T1.mgz
and brainmask.auto.mgz. Is this an appropriate solution to my
problem? The document fstutorial/skullstriptutorial, which I used as
my guide, indicates tht running recon-all with the -skullstrip flag
will generate a new brain.mgz but this did not occur when I used the
command. The autorecon help file correctly indicates that recon-all -
skullstrip generates brainmask.auto.mgz and brainmask.mgz but lacks
explanation of the command's various modes. It appears that the
generation of brain.mgz is somehow lost between autorecon1 and
autorecon2, at least in my experience.
FYI I am using freesurfer stable release 3.0.1 on a pentium 4 running
Fedora Core 4
-Tom Bayer
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