I’m having a volume mismatch between the mrtrix output and the bvec bval files. Here’s what I ran:
mrcat /AP_den_gib.mif /PA_den_gib.mif AP_PA.mif -axis 3; dwifslpreproc AP_PA.mif AP_PA_out.mif -rpe_all -pe_dir ap -readout_time 0.05 -export_grad_fsl AP_PA.bvecs AP_PA.bvals
This ran smoothly and I got the results.
I am interested in 2 files the AP_PA.mif and the AP_PA_out.mif. I converted both to .nii
The AP.mif and PA.mif files each has 160 volumes. The AP_PA.nii has 320 volumes as expected, but the AP_PA_out.nii has 160. Is this supposed to be the case? If yes, why?
When I try to run this file “AP_PA_out.nii” in FSL DTIFIT, I get a mismatch between the generated bvec/bval output of the above script and AP_PA_out.nii. The bvec/bval contain the 320 volume info is the reason, but my question is why is AP_PA_out.nii only 160 volumes? also how would I get the bvec/bval for that to use AP_PA_out.nii in FSL DTIFIT?
Thank you in advance.