 |
 |
Hi, I wouldn't say it quite like this. BBR with no fieldmaps used is definitely linear. When you add fieldmaps then it has a non-linear component due to the fieldmaps, so that the final transformations that it produces are definitely non-linear, but these transformations are generated by BBR (which combines a rigid-body transformation and the non-linear fieldmap correction). The non-linear registration provided by FNIRT, for registering the highres to the standard brain, is completely different and a separate issue. We recommend using BBR with fieldmaps (for fmri to structural registration) _and_ FNIRT (for the structural to standard registration) in order to get the best results. I hope this is a bit clearer. All the best, Mark On 8 Oct 2013, at 00:13, Matt Glasser <[log in to unmask]<mailto:[log in to unmask]>> wrote: No BBR is just linear. The nonlinear stuff is generated by field maps. Peace, Matt. From: Dianne Patterson <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Monday, October 7, 2013 5:31 PM To: <[log in to unmask]<mailto:[log in to unmask]>> Subject: Re: [FSL] BBR - linear or nonlinear? I'm under the impression that BBR calculates both the linear and nonlinear transform... and leaves you to choose what you think works best in your particular situation. I've been figuring the nonlinear is best for going from subject space to standard space... I tried both linear and nonlinear in subject space (low res to high res) and ended up thinking that the linear was fine within subject (even though epis are distorted)... That is just my take on it. -Dianne On Mon, Oct 7, 2013 at 4:08 AM, Kirstie Whitaker <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi, I'm sorry - I think this is a very simple question that I can't quite find a solid answer to in the help list. Is BBR a linear transform at the end of the day? So, for example, if I want to transform an ROI backwards into EPI space from high res space do I use convert_xfm on the <output_name>.mat file, or invwarp on the <output_name>.nii.gz file? Thank you Kx -- Kirstie Whitaker, PhD Research Associate tel: +44 7583 535 307<tel:%2B44%207583%20535%20307> Department of Psychiatry University of Cambridge Herchel Smith Building Robinson Way Cambridge CB2 0SZ -- Dianne Patterson, Ph.D. Research Scientist [log in to unmask]<mailto:[log in to unmask]> or [log in to unmask]<mailto:[log in to unmask]> University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) 621-9877 ============== Antipiphany: That moment when you realize how little you actually know ==============