Hi Seth,
I assume the image you send shows the surfaces of the two time point
taken from the *.long.baseid directories (and not from the cross
sectionally processed directories)? There are many reasons why surfaces
are different across time points. Some include
- motion artifacts in one time point, not (or less) in the other, or
other acquisition problems and non-linearities
- real atrophy
- misalignment in the base step (this is pretty rare, but you can check
the registration by switching/blending between the time points after
registration, from the .long. directories). If there is a visible global
shift or rotation, it may make sense to play around with the
robust_template command in the base to see if a better alignment is
possible, or if there are non-linearities causing the problems.
You say that when looking at individual images with surfaces, they look
spot on. That means that surfaces are created correctly, but for some
reason your images are different.
Images in the longitudinal stream should not be much more blurry as in
the cross stream. They do get interpolated to the base space, but this
is done in a single step together with the conforming. So in most cases,
there is no additional interpolation (unless images are already
conformed before, then there is a second interpolation step that could
introduce some blurring - although I think I use cubic interpolation for
that, so it should be minimal). Take a look at the surfaces in the base
(subject template) they need to be accurate there. If they include dura,
edit the base.
Best, Martin
On 02/16/2016 09:29 AM, Hutton, Seth wrote:
Hello FreeSurfers,
My lab has been using the longitudinal processing stream for our
data set and seem to be getting some potentially troublesome results.
The attached images present a snap shot of the issues we are
encountering.
As you can see in the left image, there seems to be some kind of
shifting going on. However, when you view each individual T1 with
their corresponding boundary maps they look spot on. My question is
whether or not this will have any major implication when we are trying
to do a longitudinal analysis of cortical thickness?
The more troublesome issue which is shown on the right is an overall
"messiness" that seems to occur in some scans. When looking back at
the template and the original FreeSurfer images there doesn't appear
to be any issue. It's only when the longitudinal image is constructed
that there seems to be some exaggerated blur as well as some over
inclusions of dura (this isn't shown in the image but has happened in
a handful of our subjects).
Has anyone else experienced these kinds of issues? Only a quarter of
our subjects that look as good "quality wise" as the examples posted
on your wiki.
Thanks,
Seth Hutton
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Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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