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 [ayendiki@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Douglas N Greve [greve@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
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