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 _______________________________________________ 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.
Martin,
In my experience I never found any problem in aseg.mgz
cheers
PPJ ---------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile
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 _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Allison Stevens -
Pedro Paulo de Magalhães Oliveira Junior