Hi Martin,

Thank you for your response. I assessed the QCed b-values by converting the output NRRD to FSL with DWIConvert. I was unaware only the max b-value is stored in the NRRD, which would explain the homogeneity in the b-value outputs. Given that I would like to use the QCed data as inputs to a different program to perform tractography, which requires a .nii.gz input w/ bval and bvec txt files, does DTIPrep have a method of returning all b-values (not only the max value)? I suppose a workaround would be to parse the QC report to extract the indices of slices that survive QC, and then index the original bvalue txt file accordingly.

Also, for some reason after manually setting the baseline b-values to 0, DTIPrep still did not recognize them as baseline. I only changed the .txt file; would any manipulation need to be done to the .nii as well?

Thanks,
Steven