Rejecting those volumes would likely be better than keeping them, although it means throwing out good data from the other slices in those volumes.
Tossing out the affected volumes is also easy, with fslsplit and fslmerge, and avoids registration problems.  (The motion artifacts can throw off eddy correction, esp. when they are bright, and the bad slices get mixed in with their neighbors after resampling.)

An alternative that in theory should preserve more of your data is RESTORE, which does tensor fitting with outlier rejection.  dipy has an implementation now.

     Rob

--
Robert I. Reid, Ph.D. | Sr. Analyst/Programmer, Information Technology
Aging and Dementia Imaging Research | Opus Center for Advanced Imaging Research
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org

> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Irina
> Sent: Tuesday, February 18, 2014 1:11 PM
> To: [log in to unmask]
> Subject: [FSL] DTI, "missing" slices
>
> I am a new FSL user,
> processing DTI data. I found that in some subjects, some of the volumes of
> the 4D DTI data (diffusion weighted in certain direction) look like having
> "missing slices" (actually, the slices are not completely missing, but are much
> darker than the rest of them within the same volume). What could be a
> reason for that, and what would be better to do with such volumes, to reject
> or keep?
> Thank you!