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Thank you,removing the last slice in the z-direction was my "error". Finally, I was able to correct my b0 with applytopup. But now I want to use the information from topup to correct my DWI data and when I run : applytopup --imain=DWI.nii --datain=acquisition_parameters.txt --topup=my_topup_results --out=my_hifi_images_dwi --inindex=1 I received this message: Invalid combination of phase-encode vectors for least-squares restoration. I tried to crop DWI.nii to have the same number of slice in z-direction that the b0. I alse tried to change the acquisition_parameters.txt to : 0 1 0 0.0656 But nothing works and I still have this error message. Thank for your help Arnaud 2013/6/4 Jesper Andersson <[log in to unmask]> > Yes, > > the problem here is with the odd number of slices which means it can't do > the sub-sampling in the z-direction. What I usually recommend is to collect > an even number of slices, and if not to delete one slice. Typically there > will be one slice at the top or bottom that contain mostly air. > > Jesper > > On 4 Jun 2013, at 16:42, Arnaud Boré wrote: > > Great > Thank you Jesper ! > It almost works. Now I've got the error message : Topup: > msg=topup_clp::topup_clp: Subsampling levels incompatible with image data. > > The 2 b0 are at the same resolution that my DWI's data and by default > subsampling should be 1. I tried with 1,1,1 but then I've got this error > : Topup: msg=topup_clp::topup_clp: Mismatch between --subsamp and other > parameters. > > Could you help me with that. > > Thank you > Arnaud > > > 2013/6/4 Jesper Andersson <[log in to unmask]> > >> Hi there, >> >> > I'm trying to make topup function works but I run into a segmentation >> fault error. >> > I've got 2 b0 with a different Phase Encoding (P->A and A->P) >> > >> > I created the acquisition_parameters.txt file and like the user guide >> says I can put a 1 for the fourth column but it doesn't work. >> > >> > So here is my command line : >> > >> > topup --imain=b0s.nii --datain=acquisition_parameters.txt >> --out=my_topup_results >> >> add --config=b02b0.cnf to that >> > >> > My acquisition_parameters.txt file looks like this: >> > >> > 0 1 0 1 >> > 0 -1 0 1 >> > >> > In addition, I don't understand how to calculate the fourth column so >> here the parameters of my sequence. If somebody can explain me how to do >> that. >> > >> > TR = 9300ms , TE=94ms, Echo spacing = 0.69ms, 96x96 matrix and 65 >> slices, >> > Phase partial Fourier 6/8 and finally bandwidth 1628Hz/Px >> >> the relevant time in your case is (96-1)*0.00069 = 0.0656 seconds. >> >> Good luck Jesper >> >> >> > >> > Thank for your help >> > >> > Arnaud >> > > > > -- > Arnaud BORE > Research assistant > Cellulaire : (001) 514-647-8649 > > > -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649