DWIfslpreproc TOPUP on ADNI_advanced Phillips multi shell sequence - different TEs


I am working with a Phillips scanner for the first time and am trying to implement a multi shell diffusion sequence and pipeline for some new data. Due to the lack of pre-existing protocols performed at this site, we decided to use the ADNI_adv protocol for Multishell at our Phillips scanner.

I have the following data for the main AP diffusion scan.

And then I have a reverse phase encoding scan called noFatSatA which I have been told indicates this is a PA direction scan (I have confirmed that the phase encoding looks PA). This scan does have a single higher shell (b=2000)

In terms of processing the Phillips scanner doesn’t encode some of the header information correctly unfortunately so I can’t just concatenate and use RPE_header.

Instead I used dwiextract from the main AP scan to get 6 AP b0s. Then I extract 6 b0s from the PA scan to create a b0_pair scan to run the following eddy current correction and TOPUP.

dwifslpreproc dwi_denoised_unringed.mif dwi_prep.mif -rpe_pair -se_epi b0_pair.mif -pe_dir ap -align_seepi -eddy_options " --data_is_shelled"

However, I am getting the following Warning concerning the TEs of the b0 shells between the two phase encoding scans that I want to make sure isn’t a major issue.

Could you let me know if you think this warning is something I should be concerned about?