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Hi If you are using eddy_correct, you can set the reference volume to any volume in your 4D data file. It’s the third argument in the command line tool. We do however recommend that you use the more recent tool EDDY, in which you don’t need to specify a ref volume. Instead you give eddy your bvals and it does its magic using a proper forward model for the data. Cheers, Saad > On 4 Oct 2016, at 15:26, Colleen Buckless <[log in to unmask]> wrote: > > Hi All, > I am trying to quantify the amount of motion from a DTI scan. I am aware that eddy current correction can do the correction and that there is a script that uses the ecclog files from the eddy current correction to determine the displacement relative the the first time point assuming that the first time point is the reference (B0). However, the DTI scans I am using has the B0 at the end so my reference is the last time point. Is there a way to adjust for this in determining the amount of displacement? Can I move the reference from the last time point to the first time point within the ecclog files and then run the script that has been previously provided? > Thank you for your help, > Colleen