Nope. If people get fat that does not mean that your bone marrow gets replaced.
It is, however, associated with radiation. So if someone gets a whole-brain radiation (e.g. due to metastasis, although they tend to do it less these days) you can expect such finding.
Hi again,
thank you for your comments!
Jesper, could you say a bit more about how one would experiment with the masking? Are you talking about the --inmask option of FNIRT?
I was thinking primarily of the --refmask, but yes, the --inmask might also be worth considering. If you look in the config file you’ll see an entry for the --refmask. I think that the entry is --refmask=
1,1,1,1,1,1 in
the config we ship. This essentially means that it is used for every subsampling level. You can for example change it to --refmask=0,0,1,1,1,1 which would mean that it would only be used for the 2 and 1 subsampling levels. Or even 0,0,0,0,1,1
If you can get a good mask for the --inmask that might also be worth while. For example if bet works well on your data you might try and binarise the betted brain and dilate it once and then pass that as an inmask. Again, similarly to for the --refmask,
you can experiment with when the inmask gets used.
And Andreas, thanks a lot for that information. I had no idea that was what happened. I had only noticed it used to be the case that we get lots of signal from the marrow in elderly subjects. Is this also in any way related to obesity? Shall we expect
to see this more and more?
Jesper
Thank you!
Julia
________________________________________
Von: FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag von Andreas Bartsch <[log in to unmask]>
Gesendet: Mittwoch, 30. März 2016 19:07
An: [log in to unmask]
Betreff: Re: [FSL] FNIRT registration with large ventricles
Hi,
elderly often have a high signal from the fat in the marrow of the skull
bone
Yes, because the blood-building bone marrow gets replaced by fat in the
elderly.
so first using FLIRT for registration of the functional to structural
images (Normal Search, 12 DOF)
Julia - you should use 6 (no more than 7) DOFs here because this is an
within-subject registration problem.
I assume that this won¹t solve the issue, though.
Cheers,
Andreas
Am 30.03.16, 17:03 schrieb "FSL - FMRIB's Software Library on behalf of
Jesper Andersson" unter <[log in to unmask] on behalf of
[log in to unmask]>:
Dear Julia,
elderly subjects can sometimes be a bit tricky. On the one hand the large
ventricles means that one needs to do non-lin reg. On the other hand I
have observed that elderly often have a high signal from the fat in the
marrow of the skull bone. Since that signal is not present in the MNI
template one sometimes see cases where that marrow signal at the crown of
the head gets registered to the top part of the brain in the MNI. You can
then get the effect you see.
One can sometimes solve the problem by experimenting a little with how
the masking is applied.
Jesper
On 30 Mar 2016, at 15:26, Julia Schumacher <[log in to unmask]>
wrote:
Dear FSL experts,
I am trying to do registration on data from elderly dementia patients
with quite large amounts of atrophy and enlarged ventricles.
I am performing a two-step registration procedure using the MELODIC
GUI, so first using FLIRT for registration of the functional to
structural images (Normal Search, 12 DOF) and then using FNIRT for the
nonlinear registration of structural (and functional) images to the
MNI152 template (Normal Search, 12 DOF, 10 mm warp resolution).
The first step works fine.
However, the nonlinear registration of the structural to standard image
results in bad registrations for some of the subjects where the upper
part of the brain seems to get pulled in
(https://www.dropbox.com/s/qd6krdkfvkcn2fa/highres2standard_nonlin.png?dl
=0).
We thought that the problem might be caused by FNIRT trying to align
the enlarged ventricles with the much smaller ventricles of the template
and thereby pulling the rest of the brain in.
So, I also tried using linear registration for both steps, which
results in nicely registered brain boundaries, but then obviously the
ventricles and subcortical structures are registered poorly (see
https://www.dropbox.com/s/r1dsputl0ksllw4/highres2standard_lin.png?dl=0).
Has anyone experienced similar problems with brains that show atrophy
and large ventricles?
Is there any solution to this? Specifically, is there any way to adjust
FNIRT parameters to maybe prevent this problem or to find a tradeoff
between good registration of the ventricles and good registration of the
cortex?
I would be very grateful for any help!!
I am also happy to provide more data if that helps.
Kind regards,
Julia
