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
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
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 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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