Question about empirical transmit field bias correction of T1w/T2w myelin maps

[weiwei-wch]

Hi HCP experts,
I wanna if there is an implementation of transmit field bias correction (especially the pseudo-transmit map one), Dr. Glasser published this on NeuroImage in 2022 (the preprint even much earlier), and since then I have been looking forward to the implementation, but till now I still cant find it here. Is there an implementation else where, or is there a plan for you to implement it?
And by the way our MRI data was acquired with a HCP-like protocol, which contains T1w, T2w, and AP and PA phase encoding spin echo filed map, do they satisfy the demand of the pseudo-transmit map correction?
Looking forward to your reply!

[glasserm]

At last report the releasable pipeline was about 70% done, so hopefully we are getting there soon. I apologize for the delay. You need T1w, T2w, phase reversed GRE data (e.g., fMRI) and phase reversed SE data (e.g., a spin echo fieldmap).

[weiwei-wch]

Oh it is fantastic to know that. And for the requirement of data, I only have one AP phase-encoding rest fMRI, so I need one more PA-phase-encoding fMRI to do the correction along with other data(T1w, T2w, AP and PA spin echo fieldmapm, AP fMRI)? If it is true, can a PA-phase-encoding rest fMRI with little measurements (eg. under 800ms TR, only take 60 measurements) satisfy the requirement?

[glasserm]

Actually all you need is GRE SBRefs of both phase encoding directions. The reason is that you want to balance the T2* effects across the different phase encoding directions (which are non-uniform). Alternatively, you could get a B1+ transmit map.

[roohy466]

Great, Looking forward when the script is available as I would like to compare it with Cappelle et al 2022 approach.

[glasserm]

No that method is not similar at all.

[roohy466]

Could you please clarify NO? I meant how this method comparebale with linear and nonlinear histogram calibration for T1w & T2w as described by Ganzetti et al. (2014), and also implemented in Cappelle et al 2022 .

[glasserm]

These are not even close to the same thing. Please have a close read of Glasser et al., 2022 (particularly the "theory" section) and compare with the methods sections of those two papers. After you have done that, I'm happy to address any residual questions you have.