Thanks for the suggestion Bruce! That totally solved the problem! Good to know that with the upcoming version this is solved.
Eelco
On 30 Aug 2016, at 12:36, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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.vanduinkerken@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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