Hi Guido

all automated algorithms have failure modes, so you are always advised to look at the results to make sure that they aren't artifactual. We have some QA tools that makes this process less onerous if you want. You can certainly run in an automated fashion, but then you won't know for sure if the results you found were due to an algorithmic artifact or the real biology

sorry
Bruce

On Thu, 19 Nov 2015, Guido Orlando Pascariello wrote:

Bruce, thanks for your reply

My goal about cortical morphometry is measure the mean thickness of some
areas.
Do you know if these pieces can mess up the pial surface enough to affect
the mean thickness?
I ask you about it because I am trying to avoid operator control on the
process, I want to make it automatically.

Being all for now, I await a reply

Guido PASCARIELLO
Facultad de Ingeniería - Universidad Nacional de Entre Ríos
Argentina
[mmykmWY.gif]

2015-11-19 11:02 GMT-03:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      Hi Guido

      bits of dura or skull that are left by the skull stripping don't
      matter *unless* they mess up the surfaces in the vicinity (e.g.
      by being included in the pial surface or creating topological
      defects that are incorrectly fixed).

      cheers
      Bruce


      On Thu, 19 Nov 2015, Guido Orlando Pascariello wrote:

            Hi Experts

            I'm using Freesurfer to quantify some subcortical
            volumes and cortical
            areas.

            I have been preprocessing my data using 'recon-all
            autorecon1'
            I have a question About Skullstripping. It is
            leaving a little bit of dura
            behind the head. I found '-gcut' which is useful to
            solve it but it has some
            cons.
            I don't want to view the data, I just want to get
            the quantifications, so I
            wonder if this pices of dura could affect the
            '-tessellate' step.

            I'll be grateful if you can help
            Being all for now, I await a reply

            Guido PASCARIELLO
            Facultad de Ingeniería - Universidad Nacional de
            Entre Ríos
            Argentina[mmbrzNh.gif]


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