but you'll need to convert the COR file you saved to brainmask.mgz if you
want to recover your edits (4 hours of manual editing!).
Bruce
On Wed, 28 Jun
2006, Nick Schmansky wrote:
The brainmask.mgz file is the one that should be edited (and saved), so
select that filename to save. Then just continue with autorecon2 (and
it will use your brainmask.mgz). It will not overwrite your
brainmask.mgz unless you specify the aptly named '-clean-bm' flag to
recon-all.
On Wed, 2006-06-28 at 15:00 -0400, [EMAIL PROTECTED] wrote:
I just finished my 4 hour manual editing...went to file>save volume
as...then saved it to where it defaulted me, which was the mri folder of
this subject. When i pull up my brainmask, it is giving me the same one
that it had before i made any changes. I hope i didnt do something
wrong and lost all the edits. There is 256 COR files though now in my
mri folder for this subject I noticed. Maybe these are the edited
slices? Just let me know how to get my final brainmask and how to
proceed with running -autorecon2 on it properly. Thanks.
Quoting Bruce Fischl <[EMAIL PROTECTED]>:
it helps detect cases in which the deformation is too big (e.g. when
the
surface deforms all the way into the cerebellum), and can thus
recover from
e.g. cerebellum chopping.
On
Wed, 28 Jun 2006 [EMAIL PROTECTED] wrote:
I am currently in the process of manual editing...just curious
though,
what exatly does adding an atlas do to the skullstrip process?
Quoting Nick Schmansky <[EMAIL PROTECTED]>:
First have a look at the troubleshooting wiki pages at:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
In particular, Subject 1 has a skull strip problem, and the fix
info
is
here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
I'm guessing you have seen this page since you have already
attempted
one type of fix (adjusting the watershed parameters). The
alternative
fix is the slice-by-slice manual editing.
You could also try adding the wsatlas flag:
recon-all -s (subject) -skullstrip -wsatlas
which will use an atlas to help with the skull-strip.
Does the contrast of your image look good? That is, comparing
your
orig.mgz to that of the sample subject 'bert' included with
freesurfer?
Nick
On Wed, 2006-06-28 at 10:09 -0400, [EMAIL PROTECTED] wrote:
I am having trouble with one of my skull strips, and getting
very
extreme results. When I re-run the skullstrip using different
watershed
values, anything at 56% or below takes 75%+ of the brain out,
and
as
soon as I jump to 57% or higher, it leaves on almost all of the
skull,
except for maybe 5% of it. Is this indicative of a more
complicated
problem, and what is my next step (other than manually taking
off
the
skull), if any?
Thanks
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