Hope to get your thoughts:
I've started acquiring a multi-shell DTI acquisition on our Philips 3T Ingenia (R5.3) and have encountered a small challenge in the dicom to nifti conversion.
My DTI acquisition consists of the following:
1 b=0 volume
32dir b=1000
32dir b=1500
32dir b=2000
Total vols should be 97...but I get those pesky average vols at the end of each shell (b>0) which need to be removed (and corresponding bvals/bvecs entries).
dcm2niix does a *great* job identifying the pesky vols and notifying me about them (and does remove the last shell's ADC volume):
"Note: final 1 volumes appear to be ADC images that will be removed to allow processing
Warning: Volume 33 appears to be an ADC map (non-zero b-value with zero vector length)
Warning: Volume 66 appears to be an ADC map (non-zero b-value with zero vector length)
Saving 99 DTI gradients. Please validate if you are conducting DTI analyses."

Question: Is it possible for me to somehow direct dcm2niix to remove volumes 33 and 66 (and modify the bvals/bvecs)? My workaround is to use fsl utilities...but would be great if there was a way to direct the conversion within dcm2niix.
VERSION I'm using:
MRIcroGL 64-bit Windows 7 February 2017
http://www.mricro.com :: BSD 2-Clause License
(opensource.org/licenses/BSD-2_Clause)

Many Thanks,
Jenifer