PPJ
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Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
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On Thu, May 13, 2010 at 15:28, Allison Stevens
<astevens@nmr.mgh.harvard.edu> wrote:
If you want to use the subcortical volume measures, you defnitely want to
make sure they are accurately following the intensity boundaries of the
structures. That wiki page is a little misleading in that sense (I'll work
on updating it). When I'm checking a recon for the other potential
problems listed there (skull strip issues, wm segmentation problems, pial
edits, etc.), that's when I also check the accuracy of the aseg (although
I rarely find any problems).
Allison
On Thu, 13 May 2010, Martin Ystad wrote:
> Ok, but since it does not say to routinely check it, my guess is that people
> who run hundreds of subjects through FreeSurfer (myself included) probably
> don't, which is fine since manual edits are discouraged anyway? Would another
> way of doing it be to check for outliers in the volumes produced by the
> subcortical segmentation procedure, and take a closer look at subjects that
> appear there?
>
> (There is no particular structure that appears to be inaccurate. I was just
> curious, as I'm compiling my thesis where I mention FreeSurfer-technology as
> a possible future clinical tool :)
> Thanks,
> Martin
>
> Allison Stevens wrote:
>> It should probably say to check it and make sure it is accurate although
>> you are right that we generally advise against manually editing it
>> (especially without trying automatic methods first). If there is a
>> structure you are interested in that is quite inaccurate let us know.
>>
>> On May 13, 2010, at 8:23 AM, Martin Ystad <martin.ystad@biomed.uib.no>
>> wrote:
>>
>>
>> > Maybe I've misunderstood. In
>> > http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction ,
>> > after autorecon2 it says to check white and pial surfaces before running
>> > autorecon3. The linked tutorials on how to do WM, Pial and Final
>> > surfaces edits, does not mention checking the aseg as far as I can see.
>> > Also, to express myself more clearly: I'm thinking of the labeling of
>> > the subcortical structures (thalamus, putamen, etc.). Is there something
>> > I'm missing here?
>> > - Martin
>> >
>> > Allison Stevens wrote:
>> >
>> > > It should be part of the workflow. Can you show me where it was not
>> > > listed?
>> > >
>> > > On May 13, 2010, at 7:58 AM, Martin Ystad <martin.ystad@biomed.uib.no>
>> > > wrote:
>> > >
>> > >
>> > >
>> > > > Hi, I noticed that routinely checking the subcortical segmentation
>> > > > (aseg.mgz) is not part of the Recommended Reconstruction Work Flow.
>> > > > Is this because the subcortical segmentation is highly accurate, or
>> > > > because manual intervention in the aseg is not recommended anyway?
>> > > >
>> > > > Thanks,
>> > > > Martin Ystad
>> > > > PhD-student
>> > > > University of Bergen, Norway
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>> > > >
>> > > >
>> > > >
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