Hi Martin, thank you for the response!

Here's the raw dwi.nii.gz before DWIConverting:
$ fslinfo raw_dwi.nii.gz
data_type FLOAT32
dim1 128
dim2 128
dim3 70
dim4 33
datatype 16
pixdim1 1.875000
pixdim2 1.875000
pixdim3 2.000000
pixdim4 8.844934
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+

Here it is after DWIConverting to NRRD, running DTIPrep, and DWIConverting back to NIFTI:
$ fslinfo raw_dwi_QCed.nii
data_type INT16
dim1 128
dim2 128
dim3 70
dim4 33
datatype 4
pixdim1 1.875000
pixdim2 1.875000
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+


It looks like there is change in the data_type and pixdim4. Do you think this would be an issue? And my bval and bvec files are the same before and after conversion.