I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can
comment?
On Wed, 22 Apr 2015, prasser
wrote:
Repost.Thanks.
---- On Mon, 20 Apr 2015 16:35:29 -0700 <pras...@zoho.com> wrote ----
Thank you again for your reply.
For editing aseg.mgz, as mentioned in
https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme
ntations
it does suggest using -autorecon2-noaseg, but from what I can see this
does not
update the aparc+aseg.mgz and associated .stats etc is that correct?
Doesn't
this command (as does -autorecon3) also re-create surfaces that would
need to be
re-checked and re-edited if needed?
Also, I think FS5.1 does not have the -autorecon2-noaseg flag.
As an alternative, with completed wm/pial boundaries could we run
recon-all -surfsegedit,
then we would edit aseg as needed and then:
recon-all -aparc2aseg -segstats -wmparc
This will not change any surfaces but would update aseg.stats
aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc
P
---- On Mon, 20 Apr 2015 13:42:49 -0700 Martin
Reuter<mreu...@nmr.mgh.harvard.edu> wrote ----
Hi
so take a look at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
where the entry points are described ( for brainmask and finalsurfs
-autorecon-pial should be OK, for aseg it says to use
-autorecon2-noaseg )
Also this page
https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
has details on the steps.
Best, Martin
On 04/20/2015 03:21 PM, Martin Reuter wrote:
usually edits to surfaces should not be required in the long. The
surfaces there get initialized from the base, so you need to make
sure the base surface is as accurate as possible. Several edits also
get transferred automatically from the cross sectional runs. See
this
http://freesurfer.net/fswiki/LongitudinalEdits
for a description of the different edits, and where they should be
done.
About where to restart after making the edits, everything should be
done the same way as in the regular (cross sectional) processing.
So you specifically ask about:
- brainmask edits
- brainfinalsurf edits
- and manual aseg edits.
I just looked at the description of those regular edits
http://freesurfer.net/fswiki/Edits
but sadly there it does not say where to start re-run either. I'll
try to find out and update that soon.
I hope someone with editing experience can chime in and tell us. (I
changed the subject, so that it get's read).
Cheers, Martin
On 04/20/2015 09:44 AM, Bruce Fischl wrote:
cheers
Bruce
On Mon, 20 Apr 2015, prasser wrote:
Dear All,
I wanted to check that corrections to a Long pial
surface through edits
to brainmask.mgz and brain.finalsurfs.manedit.mgz
are followed by the
command:
recon-all -long tpN1 templateID -autorecon2-pial
-autorecom3
Is this correct?
Also, after editing the Long aseg.mgz to correct
the volume of structures
what command should be run to have these edits
update the dependent files?
Thanks,
P
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-- Dr. Martin Reuter Instructor in Neurology Harvard Medical School
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ence Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology,
Massachusett
s General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technolog
y A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown,
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