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Hi, No - epi_reg won't do motion correction. If you do motion correction separately and then concatenate all the matrices together - just like this: cat *.mat > allxfms.mat then you can use this file (allxfms.mat) and the warp from epi_reg together with applywarp to resample the original, non-motion corrected 4D file with one transform. All the best, MJ On 2 Jun 2017, at 07:27, Andreas Bartsch <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Mark, no problem. Thanks. This is what I actually thought. One more question: can we supply a 4D file along with a fieldmap to epi_reg, will it then apply motion correction and unwarping to the 4D file? Many greetings, Andreas Von: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>> Antworten an: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Datum: Donnerstag, 1. Juni 2017 um 22:57 An: <[log in to unmask]<mailto:[log in to unmask]>> Betreff: Re: [FSL] epi_reg Hi, Sorry for the delay in responding. This is for incorporating gradient non-linearity distortion correction. The warpfield can be calculated by the MGH tool gradient_unwarp.py (which is also used in the HCP) although it requires a file of coefficient values that relate to the gradient coil that you need to obtain from Siemens, as it cannot be shared. All the best, Mark On 19 May 2017, at 16:26, Andreas Bartsch <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello, what is --gdc=<image> : Gradient-distortion corection warpfield in the latest epi_reg for and how do you generate the warpfield? Cheers, Andreas