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Do you have the GRE fMRI phase encoding right, the order of the SE scans right for topup, the correct echo spacing for the GRE fMRI, and the correct total readout time for the SE scans? All of these things will influence the distortion correction if you do it in this way. Then ideally you will use BBR for EPI to T1w registration, which is more accurate than other methods. fslreorient2std is a good idea to run on all your raw scans before processing them. Matt. On 3/12/19, 2:04 AM, "FSL - FMRIB's Software Library on behalf of Conrad Rockel" <[log in to unmask] on behalf of [log in to unmask]> wrote: >Hi folks, > >My main question is: how much does the registration to T1 matter when >applying the TOPUP field map (w/ Hz-to-rads) to a same-session fMRI >dataset? > >My topup-derived fieldmaps are making things worse regarding OFC >geometric distortion, and I'm pretty sure that my choice of timing >parameters is ok. > >When I check the Registration/Unwarp HTML output, the registration for >"fieldmap_to_hires" (at home, don't have access to precise filenames) is >definitely off, especially in the z-direction. I read a post on the FSL >forum about this today regarding what registrations to check, which I >then lost (GRRR!). Could anyone remind me what files to check, or a link >to THAT post if you recall? > >My secret suspicion is that (if a registration to T1 issue) our T1s are >collected sagittally (although I used 'fslreorient2std' on this volume). >This gives a lot of extra neck. I then used SPM for skull stripping, >which may have screwed things up further re: origin/sform/qform). Our >scanner (GE 750 3T) produces axial volumes for the sagittal acquisition, >and I wonder if I should be trying with those? > >Thanks in advance, > >Conrad > >######################################################################## > >To unsubscribe from the FSL list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1