I would like to use TORTOISE on a data set for which T1, and not T2, structural data were collected. I read about a work-around for using T1 images here which seems to involve attenuating non-brain regions. Apparently this suggestion came from a TORTOISE developer. I just want to make sure that this would be valid and/or necessary to do in the most recent version of TORTOISE (3.2.0 at time of writing).
To partially answer my own question, it seems like some kind of T1 inversion algorithm to approximate T2 is valid enough to get published (https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.23318 - Appendix A), but I would still like to know about the pipeline outlined in the link in the original question is alright, since the code there is written out.
If you are willing to use the T1W-inverted image for EPI distortion in DIFFPREP, I would say that is not a good idea at all.
DRBUDDI, with blip-up blip-down data is more robust at this. What I would suggest is to try it with one data and examine the results though.