Hi Muskan,
Excellent question, thanks for formulating it so clearly. I have experimented with several of these options and I find that approach 5 works best, at least for a “standard” protocol with a AP-PA pair as you’re describing. You can pass these AP-PA b0 images separately to dwifslpreproc using the -se_epi option.
Some thoughts about why we prefer option 5:
- Options 1 and 2 won’t do much of denoising on the AP/PA b0 volumes because the no. volumes (4) is too small.
- Options 3 and 4 can potentially be problematic because the AP-PA geometry shift increases the local rank of the signal and may as a consequence lead to an underestimation of the noise level.
- Option 5 distinguishes between the field map estimation, based on the AP-PA images, and the denoising & geometry correction of the dMRI data that will be used in further analyses. The field map estimation is strongly regularized so not too sensitive to noise; besides, the b0 images are of high SNR anyways. Its output is then used as an input to the main data processing pipeline, in which in this case the noise level estimation is done entirely independently.
Cheers,
Daan