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Hi, The PET image with the ROIs is aligned to the T1 with FLIRT. So all I need to do is to align the FA/MD to the TI using FLIRT as well. It is the same brain so i cannot see any reason to use FNIRT. Yes, I agree. Unfortunately the sampling was done without reversing the phase coding so Top up is hard to apply unless one tries the T2 image. I have tried that before, with help from Jesper Andersson, but the distortions were not corrected to any larger degree. That's a pity if you cannot correct for the distortions and they are noticeable in areas that you care about. I understand doing the b0 (aligning to the T1) first and then running eddy and the rest of the preprocessing into FA. Or only aligning the final FA. But in the latter case, the B0 will not be aligned to the T1. Or how do you mean? When you run eddy it should align everything with the b0 scans, so that the FA derived from eddy output will be aligned with the b0. Hence it shouldn't matter whether you align the FA to the T1 or the b0 to the T1, as long as the b0 is the one that eddy uses as the reference (the first one). All the best, Mark best nick Niklas Lenfeldt, PhD, MSc E.P Umeå University Phone: +46706096687 ________________________________ Från: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> för Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>> Skickat: den 16 september 2018 11:17 Till: [log in to unmask]<mailto:[log in to unmask]> Ämne: Re: [FSL] Registration to T1 Hi, I am wondering, we are going to register FA images to T1 and PET images and I am wondering when in the process this is preferred to be carried out? It doesn't really matter when you perform registration compared to other steps - what really matters is what images you use to do the registration and whether you resample (transform the images into another space) prior to any other processing steps or not. We have ROIs outlined in PET where we want to assess FA in the sane areas. That's fine - you just need to have transformations that can take you from PET space to FA space (or vice versa) and then apply this to the ROI. Before the DTI images are processed into FA, MD etc or after? OK, in this case you want to do the preprocessing of the diffusion images first (i.e., motion correction, eddy current correction, geometric/susceptibility/B0 distortion correction). Then you can either use the preprocessed images directly (typically the b0) or calculate the FA and use that. Either is fine and we've seen different results from different scanners and protocols so that it is hard to say for sure which is best. I would typically try the b0 image first, but trying both and then comparing the results is probably the best approach. What you want to do is to register a diffusion image to the T1 and then, independently, the PET to the T1. Once you have both then you can combine the transformations to move between any pair of spaces. I hope this helps. All the best, Mark Best Nick ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1