Dear Bruce, thank you for your fast and helpful response.
I have read in some papers (e.g. paper1 <https://scholar.google.com/scholar?hl=en&q=Validation+of+hippocampal+volumes+measured+using+a+manual+method+and+two+automated+methods+%28FreeSurfer+and+IBASPM%29+in+chronic+major+depressive+disorder&btnG=&as_sdt=1%2C5&as_sdtp=> ,paper2 <https://scholar.google.com/scholar?q=Evaluation+of+Hippocampal+Volume+Based+on+Various+Inversion+Time+in+Normal+Adults+by+Manual+Tracing+and+Automated+Segmentation+Methods&btnG=&hl=en&as_sdt=0%2C5>) 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 <fis...@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 >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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