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Hi there Stefano, > Is this patch for eddy already available? we are working intensely on it, but it is not finished just yet. > Another question I have is the following: would it be possible (or even a sensible thing to do) to create individual top-up distortion maps for each pair of diffusion weighted images (blip-up and down), and then correct each pair individually with top-up. Shouldn’t this do the same job as eddy? Just to add to Matt's point here. In principle you are right that if you have blip-up and blip-down for each direction then that pair would allow you to estimate both susceptibility and EC distortions. The information in such a pair is part of the information that is used inside eddy. There are a few caveats to that though 1. It still doesn't give you any information of the position of this pair relative to other pairs (i.e. subject movement). 2. If one of the volumes in that pair has artefacts such as e.g. slice drop-out it will cause problems. In eddy we are considering all the images at the same time so an artefact can be quite easily identified by virtue of "voting". Jesper > Stefano > > From: Jesper Andersson [mailto:[log in to unmask]] > Sent: Wednesday, October 24, 2012 9:48 AM > To: [log in to unmask] > Subject: Re: [FSL] problem in running eddy > > Hi again, > > > > eddy --imain=DWIseries --mask=brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=topup_output --out=eddy_out > > and after an hour or so got the following error message: > > Terminate called after throwing an instance of ‘NEWMAT::IndexException’ > > I'm afraid I have a very good idea. There is a bug in the post-processing of the eddy parameters that causes this. We have fixed it and it will be part of an upcoming release of fixes. Sorry for that. > > Jesper > > > > > Any idea of what could have gone wrong? > > Stefano Marenco, MD > NIMH/CBDB > 10 Center Drive, Bldg 10 room 3C103 > Bethesda MD 20892 > Tel 301 435-8964 > Fax 301 480-7795 > Email: [log in to unmask] > >