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You are absolutely correct I did not patch my eddy. thanks a lot. *Michel Thiebaut de Schotten* Associate Professor, PhD, HDR, CNRS Sorbonne Universities, UPMC Univ Paris 06 Brain Connectivity and Behaviour Group Institut du cerveau et la moelle épinière Hôpital de la Salpêtrière - ICM 47 Bvd de l'Hôpital CS21414 75646 PARIS CEDEX 13 Skype: michel_thiebaut_de_schotten phone: +33 7 83 50 81 60 http://www.bcblab.com http://toolkit.bcblab.com <http:/toolkit.bcblab.com> On Fri, Mar 17, 2017 at 4:30 PM, Jesper Andersson < [log in to unmask]> wrote: > Dear Michel, > > the --data_is_shelled option came with the 5.0.9 eddy patch ( > fsl.fmrib.ox.ac.uk/fsldownloads/patches/eddy-patch-fsl-5.0.9/). Are you > sure you are using the right version. > > Jesper > > > On 17 Mar 2017, at 13:47, Michel Thiebaut <[log in to unmask]> > wrote: > > Dear experts, > > I've been running eddy on a multishell dataset but eddy indicates that my > data is not shelled (error report below). > I tried the --data_is_shelled, but eddy does not recognise this option > (--data_is_shelled: Option doesn't exist!) > > I was wondering whether somebody had the same problem and/or could help me > find out a solution. > > Thanks a lot > > michel > > eddy --imain=data --mask=my_hifi_b0_brain_mask --acqp=acqparams.txt > --index=index.txt --bvecs=bvecs --bvals=bvals --topup=my_topup_results > --out=eddy_corrected_data -v > Reading images > Running Register > Loading prediction maker > Evaluating prediction maker model > Calculating parameter updates > Iter: 0, Total mss = 551.67 > Loading prediction maker > Evaluating prediction maker model > Calculating parameter updates > Iter: 1, Total mss = 549.76 > Loading prediction maker > Evaluating prediction maker model > Calculating parameter updates > Iter: 2, Total mss = 547.861 > Loading prediction maker > Evaluating prediction maker model > Calculating parameter updates > Iter: 3, Total mss = 547.686 > Loading prediction maker > Evaluating prediction maker model > Calculating parameter updates > Iter: 4, Total mss = 547.758 > Running sm.Setb0Reference > Running sm.PolateB0MovPar > Running Register > Loading prediction maker > Evaluating prediction maker model > I'm thrown > libc++abi.dylib: terminating with uncaught exception of type > EDDY::KMatrixException: KMatrixException: msg=MultiShellKMatrix::SetDiffusionPar: > Data not shelled > Abort trap: 6 > > > > *Michel Thiebaut de Schotten* > Associate Professor, PhD, HDR, CNRS > Sorbonne Universities, UPMC Univ Paris 06 > Brain Connectivity and Behaviour Group > Institut du cerveau et la moelle épinière > Hôpital de la Salpêtrière - ICM > 47 Bvd de l'Hôpital CS21414 > 75646 PARIS CEDEX 13 > > Skype: michel_thiebaut_de_schotten > phone: +33 7 83 50 81 60 > http://www.bcblab.com > http://toolkit.bcblab.com > > >