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Dear FSL experts, I want to align (intra-subject) a DWI with an AC-PC oriented T1 image. Epi_reg seems to be a good choice for that, but as far as I know I should rotate the gradient table after that. I first process the DWI with topup and eddy, and then use epi_reg. I know that eddy rotates the bvecs for me, but I think they have to be rotated again after epi_reg? How would you do this? epi_reg also creates a new file with the same dimensions as the T1 (resulting in upsampling from 2x2x2 to 1x1x1). Is this advisable, or is there a way around this? (Background: I would like to match a mask created with the T1 image as closely as possible to the DWI to run a clustering algorithm (on ODFs created in qboot). A better spatial resolution would of course help with that.) Thank you in advance :) Cheers Melanie ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1