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Thank you very much for your help!! It's very much appreciated. 2017-08-22 6:13 GMT-04:00 Jesper Andersson <[log in to unmask]>: > Dear Arnaud, > > >> Dear Arnaud, >> >> > Correct me if I'm wrong: looking at the FSL mailing list I've seen that >> if you acquire an odd number of slice (z axis) you need to remove one slice >> (top or bottom) in order to use topup. >> > >> > There is one other solution which is to modify the Subsampling level >> 2,2,2,2,2,1,1,1,1 to 1,1,1,1,1,1,1,1,1. It is way slower than removing one >> slice and I'm not sure the result will be as good as removing one slice. >> > >> > My question is: can I consider adding a slice of zeros instead of >> removing one slice if my FoV is too tight ? >> >> I think your best solution is to do what you suggest with the subsampling >> levels. If you also change the --lambda values for the first 5 steps you >> should get just as good results, and all you pay will be execution time. >> > > > I've run topup with and without removing the top slice. I've got 3b0s ap > and 9 b0s pa. It took 1h (after removing one slice) and 4h (without > removing the top slice) to run topup. The results were similar (even slices > gives smoother results) but the resulting images are cropped top and bottom > (+/- 1-2 slices). Is this "normal" ? Is there a better way to run topup ? > > > it sounds like some serious overkill to run topup on 3+9 volumes. My > experience from any half decent SNR data is that 1+1 is usually enough, > possibly 2+2 if you are pressed for SNR. That would reduce your execution > time a lot. > > The cropping comes from topup only considering the estimated field valid > for voxels that fall within the FOV for all volumes in the input. Consider > for example if you have two volumes (one each in AP and PA) and the subject > slides down (translation in the z-direction) two slices between the AP and > the PA. That means that in the PA we have not acquired the two bottom > slices that we acquired in the AP, and hence we have no way of knowing what > the field is in those two slices. topup will then set the output to zero > for those two slices. > > > >> >> For getting the --lambda values ~right I suggest you do a test run with >> 2,2,2,2,2,1,1,1,1 and 1,1,1,1,1,1,1,1,1 for a subject where you have >> removed one slice and use trial and error to change --lambda so that you >> get ~the same reduction in SSD for the first five steps in both cases. > > >> > Thank you for your suggestion, I think it will be complicated to change > lambdas since I've no idea of how each of them will have an impact on the > resulting images. Especially if each trial takes 4h to run. > > > I will run some tests so I can make a .cnf file also for the case when > people have an odd number of slices. > > Jesper > > > Thank you again for your help > Arnaud > > Jesper >> >> >> > >> > Thank you in advance for your help. >> > >> > Arnaud Bore >> > > > > -- > Arnaud BORE > Research assistant > Cellulaire : (001) 514-647-8649 <(514)%20647-8649> > > > -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649