Hello freesurfers Does anyone knows wich is the method in which the FS makes an average of 2 images, in the autorecon1 step when doing the motion correction?. I mean how can I explain it?
Thanx Gabriel
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Hi Gabriel,
I'm pretty sure we use FSL's flirt for motion correction by default, but Nick or Doug can confirm.
cheers Bruce
On Thu, 1 Jul 2010, Gabriel Go.Es. wrote:
Hello freesurfers Does anyone knows wich is the method in which the FS makes an average of 2 images, in the autorecon1 step when doing the motion correction?. I mean how can I explain it?
Thanx Gabriel
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Thank you Bruce for you answer, but i still have the doubt, is motion correction from the FSL the method to average the images? or is another method... I wrote motion correction cuz in the -help of recon-all says that theyr made in the same step, but not to be the same process. but whatever is not explain which is the averaging method, even when i look in the FS page, it appears the mri_average, but has no methodology explained.
Best Gabriel
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Hi Gabriel,
I'm not sure I know what you mean. I think we use flirt to compute the motion parameters, then we just average the images in the aligned space (which I think is to the first scan specified, but Doug would know)
cheers Bruce On Thu, 1 Jul 2010, Gabriel Go.Es. wrote:
Thank you Bruce for you answer, but i still have the doubt, is motion correction from the FSL the method to average the images? or is another method... I wrote motion correction cuz in the -help of recon-all says that theyr made in the same step, but not to be the same process. but whatever is not explain which is the averaging method, even when i look in the FS page, it appears the mri_average, but has no methodology explained.
Best Gabriel
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yes, the first image is the template. I think it uses flirt. Recent versions may use Martin's robust registration.
doug
Bruce Fischl wrote:
Hi Gabriel,
I'm not sure I know what you mean. I think we use flirt to compute the motion parameters, then we just average the images in the aligned space (which I think is to the first scan specified, but Doug would know)
cheers Bruce On Thu, 1 Jul 2010, Gabriel Go.Es. wrote:
Thank you Bruce for you answer, but i still have the doubt, is motion correction from the FSL the method to average the images? or is another method... I wrote motion correction cuz in the -help of recon-all says that theyr made in the same step, but not to be the same process. but whatever is not explain which is the averaging method, even when i look in the FS page, it appears the mri_average, but has no methodology explained.
Best Gabriel
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OK, so the alignment is to perform a simple average? that way, the real goal of the method is the registration before averaging, am I right? in versions like 4.05 what was the alignmen method, was the flirt? Do you know if Martin's robust registration is now implemented or will come in the next version of FS?
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Gabriel Go.Es.