Dear Bruce,

thank you for your fast and helpful response.

I have read in some papers (e.g. paper1,paper2) that FreeSurfer overestimates hippocampus volume a little compared to the manual segmentation. I know this is to be expected, but I wanted to see if there are some parameters that I can work with to reduce this problem as much as possible.can I access to probabilities which computed for subcortical segmentation from training data in FreeSurfer ?

Sincerely,
Nazanin

On Sun, Jun 19, 2016 at 7:21 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Nazanin

no, sorry, that isn't possible. Our accuracy is improved by the fact that we model all subcortical structures simultaneously.

As for your second question you need to be more specific. Are you finding some inaccuracies that you want to correct?

cheers
Bruce

On Sun, 19 Jun 2016, N Saf wrote:

Dear Freesurfer,

I wonder if it is possible to segment just one sub-cortical structures like
hippocampus by changing the algorithm (e.g. according to spatial prior
knowledge divided the image to some sub-images and do analysis just on that
sub-image which we sure the hippocampus located)and by that reducing the
processing time ? and another general question I have is that in
sub-cortical segmentation commands 1to12 commands of -all flag which
parameters can I change to affect the outputs?

Sincerely,
Nazanin

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