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 <fis...@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.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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail.
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