Hi Nazanin
those steps are already incorporated into recon-all - you don't need to
do anything special
cheers
Bruce
On Fri, 20 Jan 2017, N Saf wrote:
Dear Bruce,
I read this article "Atlas Renormalization for Improved Brain MR Image
Segmentation Across Scanner Platforms(2007)" and I wonder if theses steps
"normalization" and "normalization2" do the Atlas Renormalization which
mentioned at that article or should I use another command myself to do the
Atlas Renormalization that the article proposed? (sorry if the question is
basic)
Best,
Nazanin
On Fri, Jan 20, 2017 at 9:16 AM, N Saf <nali...@gmail.com> wrote:
Dear Bruce,
thank you for your comprehensive explanation.
Best,
Nazanin
On Thu, Jan 19, 2017 at 7:00 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Nazanin
there is no easy way to display a partial volume. You can
still use Dice/Jaccard on the hard segmentations, but we
have found that the partial volume correction improves
e.g. test/retest reliability and probably accuracy,
although that is harder to prove.
cheers
Bruce
On Thu, 19 Jan 2017, N Saf wrote:
Dear Bruce
is there any 3D image file which shows the
segmentation regions after this
correction ?and if there is not is it right to
use aseg.mgz file for
reporting Dice or Jaccard Index (I have manual
segmentation as gold
standard)?
Best Regards,
Nazanin
On Wed, Jan 18, 2017 at 5:18 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Nazanin
the volumes reported in the aseg.stats
file have been corrected
for partial volume effects.
cheers
Bruce
On Wed, 18 Jan 2017, N Saf wrote:
Dear FreeSurfers,
I have a question about aseg file.
I load the aseg
file of bert subject in
itk-snap and read the volume for
17 and 53 label but
it is a bit larger of
the volume in bert stats file. I
do the same for
some of my subjects too and
I see the same result .I don't
know why it is like
that ?would you please
clear the reason for me.because I
need to compare
the FreeSurfer result and
I should use of aseg file labels
but I'm afraid the
comparison I'm doing is
not valid.
Sincerely yours,
Nazanin
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