> > Hi, > > we have more motion in the anatomical data between the groups (healthy > controls vs patients). > The difference between 5.1 using flt and 5.2. using bbr is not extreme. > If I understood correctly, since we use first recon-all and thatis > independent of flt or bbr, any difference musts come how the two algorithms > deal with the dti raw data. Is there any motion correction? > The preprocessing steps include eddy current correction but I did not find > a step for motion correction. > > Regards > Gerit > ________________________________________ > Von: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Gesendet: Dienstag, 16. Juli 2013 20:03 > An: Roschinski, Benjamin > Cc: freesurfer@nmr.mgh.harvard.edu; Pfuhl, Gerit; King, Joseph > Betreff: Re: [Freesurfer] motion dependent resolution: bbr vs flt > > Hi Benjamin - You can see how bbregister works in this paper: > > http://surfer.nmr.mgh.harvard.edu/pub/articles/greve.2009.ni.63.BBR.pdf > > In short it uses the surfaces from the freesurfer recon (which of course > come from the anatomical) to align the anatomical to an EPI (in this case > the low-b from the diffusion series). Because bbregister uses the extra > information about the surfaces (which flirt doesn't), that's why Doug was > asking if the motion is in the anatomical or the diffusion. > > Between 5.1 and 5.2 several things changed in tracula, only one of them > being the default registration method. You can still switch back to flirt > with 5.2 though if you want to check if that's what's making the > difference. The instructions for this are under "Specify the intra-subject > registration method" here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > Let me know if you have any other questions. > > a.y > > On Tue, 16 Jul 2013, Roschinski, Benjamin wrote: > > > Hi Doug, > > > > thanks for the answer. > > We did a comparison between the results of TRACULA 5.1 and 5.2. > > When we compared the two different results (5.1 and 5.2) from health > controls and recovered anroxia nervosa patients for the first time the > results of TRACULA 5.2 seemed to be better than the ones of TRACULA 5.1 > > Then we did the same with our acute anorexia patients which are less > settled in mri studies. > > In the end the TRACULA 5.2 outputs were not as good as the results of > TRACULA 5.1 after we included the acute patients. > > I hope now you understand why we thought that bbr might be more > sensitive for motion. > > If bbr is pretty robust in anatomical and dti what do you think about > flt. Is it as good as bbr or might be better in case of motion? > > Another question: we know that bbregister needs to have a high > resolution image reference for its algorithm. > > Is that the T1? > > > > thank you very much > > > > Benjamin > > > > ________________________________________ > > Von: freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von > "Douglas N Greve [gr...@nmr.mgh.harvard.edu] > > Gesendet: Montag, 15. Juli 2013 19:41 > > An: freesurfer@nmr.mgh.harvard.edu > > Betreff: Re: [Freesurfer] motion dependent resolution: bbr vs flt > > > > Hi Benjamin, BBR does not need higher resolution. Do you mean motion in > > the anatomical or motion in the DTI? BBR should be pretty robust in > > either case. It is hard to know what might be going on without more > > details of why you think it is getting worse. > > doug > > > > > > On 07/14/2013 08:01 AM, Roschinski, Benjamin wrote: > >> Dear freesurfer experts and users, > >> > >> we visualize white matter tracts of anorexia nervosa patients which > >> are characterized by more movements in mri studies. > >> We have the impression that we get worser TRACULA outputs by using > >> bbregister than flt. > >> Could it be possible that bbregister needs a higher resolution than flt? > >> So summarizing it is more sensitive for motion? > >> > >> kind regards > >> > >> Benjamin > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > 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 . 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. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >
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