mtnormalize for DWI


I am interested in applying mtnormalize directly to 4d DWI data rather than the fod and was wondering-

  1. if for some reason this wasn’t sound? From what I can tell, it at least does a beautiful additional inhomogeneity correction.

  2. if I wanted to apply another multi-tissue model down the line, is there some way to take advantage of various tissue compartment inputs, again, in the context of a DWI input rather than the fod?

Any advice would be greatly appreciated!

Thanks so so much in advance

Welcome @T.M.N!

I am interested in applying mtnormalize directly to 4d DWI data rather than the fod

I can read this two ways:

  1. You want to use DWI data to estimate a bias field.
    The very premise of the mtnormalise algorithm is that there are certain expectations of the data following a multi-tissue decomposition that are broken in the presence of a bias field, and therefore enable estimation of that field. Without a multi-tissue decomposition however, the theory is inapplicable from the outset.

  2. You want to apply the bias field estimated by mtnormalise to correct for the bias field in DWI data.
    This is easy: The -check_norm option outputs the estimated bias field, which can then be applied to the DWIs from which the ODF images were estimated.


Thank you so much for your quick and helpful response! I am so sorry to have missed this and come back to it months later (many apologies). You did in fact answer my question in 2 and I was easily able to use the the multi-tissue bias field output to correct my DWI (!!).

@Julio_Villalon and I do have a very naive follow-up question: as I mentioned, the first time I attempted this by just supplying the full DWI to mtnormalise rather than each tissue FOD. The output DWI somehow actually looked quite reasonable–i.e.normalized values and fewer inhomogeneities. I’m a bit embarrassed to ask, but could you confirm whether or not that output is “usable”/what mtnormalise does in that case? I understand from your response that it requires a multi-tissue decomposition to properly estimate the field as described, but would the output DWI be nonsense or usable for further analyses?

Thanks again for your time and help