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Hi Jesper, Thanks for your prompt reply! Now I see. Yes, this is multi-shell data. These two shells (b-value = 1300 and 1400 s/mm2) have 32 directions. Do we have a guideline on what is the minimum angular sampling given a b-value? For example, how does EDDY determine whether a shell should be included in the predictive model or not. It’ll be very informative for future protocol setup. Really appreciate it! Best, Qiuyun From: Jesper Andersson [mailto:[log in to unmask]] Sent: Wednesday, February 08, 2017 6:20 AM To: Fan, Qiuyun Cc: [log in to unmask] Subject: Re: eddy_openmp Dear Qiuyun, are you sure these data are actually multi-shell (as opposed to DSI)? The predictive model inside eddy is based on the data residing on a limited number of shells where each shell has a “reasonable” angular sampling (exactly what is reasonable depends on the b-value of the shell). If the data doesn’t conform to that model eddy will perform less well. It would be my first guess that this is what you are seeing. It is on my “to do list” to come up with a predictive model for DSI data, but we all know how those lists work :( Jesper On 7 Feb 2017, at 18:54, Fan, Qiuyun <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL experts, I used eddy_openmp to preprocess a multi-shell dataset. The corrected data looks great except for two shells. I checked the *.eddy_parameters output, and found the 7th - 15th elements are all zero for volumes of these two shells (b-value = 1300 and 1400 s/mm2). Other shells, higher or lower than b-value = 1300 and 1400 s/mm2, gave close to zero but non-zero elements, which look fine. Do you have a hint on what might be the cause, by any chance? Thanks a lot! Here’s the command I run: eddy_openmp --imain=diff_AP_b0s_PA.nii.gz \ --mask=hifi_b0s_avg_brain_mask.nii.gz \ --index=index.txt \ --acqp=topup_acqparams_b0s_AP_PA.txt \ --bvecs=bvecs_diff_AP_b0s_PA.txt \ --bvals=bvals_diff_AP_b0s_PA.txt \ --out=hifi_diff_AP_b0s_PA \ --flm=quadratic \ --topup=topup_b0s_AP_PA \ --interp=spline \ --data_is_shelled –v Best, Qiuyun The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.