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 7^th - 15^th 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