Hi Chris,
I'm a longtime user of MRIcro, MRIcron, and dcm2nii...Really like your MRIcroGL tool with dcm2niix! Super fast and outstanding ease of viewing :)
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 edited).
dcm2niix does a *great* job identifying the pesky vols and notifying me about them (and removes 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)?
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)

Really appreciate your thoughts...
Cheers,
Jenifer

The latest versions will create a copy of your images that removes all derived volumes from Philips DTI data. However, you should also contact Philips, as they are violating the DICOM standard: derived data MUST be stored with a separate series number than the raw data.