the QC on the T1 data gives no obvious clue. We edit the brainmask when there are surface issues However, we have not quantified this data yet - a closer look may indeed tell us more.
Thanks Gerit On 16 July 2013 20:52, Pfuhl, Gerit <gerit.pf...@uniklinikum-dresden.de>wrote: > > ________________________________________ > Von: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Gesendet: Dienstag, 16. Juli 2013 20:51 > An: Pfuhl, Gerit > Cc: Roschinski, Benjamin; freesurfer@nmr.mgh.harvard.edu; King, Joseph > Betreff: Re: AW: [Freesurfer] motion dependent resolution: bbr vs flt > > Is the motion in the anatomicals bad enough that it would affect the > quality of the surfaces? Bbregister uses the surfaces, flirt does not. > > The "eddy current correction" is also motion correction - it aligns all > the frames to the first with an affine registration. Rotation and > translation due to head motion, in addition to warping due to eddy > currents, is what cause the frames to be misaligned. It's assumed that by > aligning them you correct for both (approximately). > > On Tue, 16 Jul 2013, Pfuhl, Gerit wrote: > > > 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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