Hi Eelco
we've made a bunch of improvements in the T2/FLAIR stream since 5.3 so you
might check them out. Unfortunately I don't think they will be officially
supported in 6.0 as we just don't have the resources to include it in our
unit/system/regression test cycle.
cheers
Bruce
On Tue, 30 Aug 2016, Eelco van Duinkerken wrote:
Dear all,
Sorry for spamming, as I have posted this message about 2 weeks ago, but
didn't receive an answer just yet.
I probably did something wrong :).
I've been preprocessing, in FS5.3, 3T GE data in controls, obese and
diabetes patients and adding the available flair to do the pial refinement
as follows:
recon-all -i t1 -s participant -all -FLAIR flair -FLAIRpial
This works excellent for most of the scans. Unfortunately, for some scans
adding the flair leads to some interesting refinements, either extending
outside of the brain.mgz or going deep into the white matter.
I didn't notice any misregistrations of the flair to the T1 scan when
checking the bb-registration. I have added some screenshots and the
recon-all.log files. The red lines represent the pial with the flair
refinement, and the blue lines the pial without the refinement. As you can
see, these interesting segmentations are not there when the flair is no
used.
Does anyone know what is going on?
Thanks a lot,
Eelco
--
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 22451-900 |
Brasil |
E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
http://lattes.cnpq.br/7180895567820901
&
VU University Medical Center | Department of Medical Psychology |
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands
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