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Hi Steve, I think their after rotating the diffusion gradient vectors (i.e. the bvecs file) rather than something like the data_V1.nii.gz file. This isnšt something we do in the HCP Pipelines either, but the code to do it for a single transformation matrix (e.g. raw diffusion space to T1w native space) exists and could be adapted for this purpose: https://github.com/Washington-University/Pipelines/blob/master/global/script s/Rotate_bvecs.sh I donšt have a good sense of how much difference this makes. Perhaps some enterprising soul will try this on HCP data and show how much it reduces dispersion or otherwise improves bedpostX estimates Peace, Matt. From: Stephen Smith <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Thursday, April 23, 2015 at 1:08 AM To: <[log in to unmask]> Subject: Re: [FSL] Eddy current correction- rotation of encoding vectors? Hi - see the manual: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#vecreg_-_Registration_of _vector_images Cheers > On 23 Apr 2015, at 06:37, Manaal Fatima <[log in to unmask]> wrote: > > Hi all, > > When correcting for eddy currents, I understand that FSL affine registers the > diffusion volumes to the reference volume with no diffusion weighting, which > involves some sort of transformation/rotation. Several papers have noted that > if a transformation/rotation has been applied to the image, then the same must > be applied to the encoding vectors. My understanding is that these "encoding > vectors" are simply the gradient directions applied during acquisition of the > diffusion-weighted volumes (bvecs). However, I can't seem to find any info on > whether or not this has been factored into FSL. If it hasn't, how do people go > about applying the same transformation to the bvecs file prior to fitting > diffusion tensors or running tractography? > > Thanks in advance! > > Manaal --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net>