Processing of volumes prior to dwipreproc

preprocessing

#1

Hi,

Thank you very much for the tutorial. I had a single doubt regarding the AP and PA volumes for dwipreproc. Since the AP images extracted from the DWIs have already undergone a series of preprocessing steps(dwidenoise and mrdegibbs namely), should the PA images go through the same steps as well before they are concatenated for use with dwipreproc?

Regards,
Archith


MRtrix tutorial available on OSF
#2

(Moved to new topic since question is not specific to the title of the thread in which it was posted)

If they are being used together, then ideally yes. Gibbs ringing removal is easy; the hard part is denoising, which you cannot perform on one or a small number of b=0 volumes in isolation:

  • If you are explicitly yourself combining copies of one or more of the AP b=0 volumes from the DWIs with one or more PA b=0 volumes, then you can omit the denoising step from processing of just that set of volumes.

  • Personally I expect the spatial distribution of noise level to be more-or-less equivalent across image volumes regardless of phase encoding direction, and therefore concatenate all volumes in order to perform denoising and then separate the volumes out into “DWIs to be corrected” and “spin-echo EPIs to be used to estimate the inhomogeneity field”. However if you have a scanner that may grossly adjust image intensities in between protocols, this may be problematic.

Realistically though, I’m not sure exactly what type of ‘bias’ may be introduced by having a greater level of noise in volumes with one phase encoding direction than those with the opposing direction…


#3

Thanks for the clarification. I would like to carry on with the two approaches

Explicitly combine AP and PA b0s after mrdegibbs on each ; Pass them to the dwipreproc step with input as the mrdegibbs and dwidenoised data and the undenoised AP-PA concatenated data as the -rpe_pair -se_epi option

After checking the mean intensities of AP and PA b0 volumes.

Would any differences between 1 and 2 hint something about this? What would you suggest?

Thanks and Regards,
Archith


#4

… as the mrdegibbs and dwidenoised data …

Just confirming that dwidenoise cannot be applied after mrdegibbs (or basically any other process).

After checking the mean intensities of AP and PA b0 volumes.

I believe that topup estimates a global scaling factor between image volumes. Don’t quote me on this though.

Would any differences between 1 and 2 hint something about this?

No, the difference between 1 and 2 would be due to estimating the inhomogeneity field from denoised or not-denoised data. What I was referring to specifically in that comment was what might happen if the AP volume(s) is/are denoised but the AP volume(s) is/are not. It would certainly have an effect, I’m just not sure if there would be a ‘bias’ strictly.


#5

Thank you very much for the clarification.I’m sorry I messed up with the order of denoise and mrdegibbs earlier… meant the other way round.

Regards,
Archith