Help with HCP 7T data

Hi all,

I am currently trying to work on HCP 7T diffusion MRI data but happen to find out that the b0 signal in the frontal and temporal lobes are very small (those areas appear to be very dark). This causes serious problem for the next step of model fitting in those areas. For example, the FA map looks wired. Is there any way to tackle with this problem?

Thanks a lot in advance~~~


Here is an exemplary FA map from HCP 7T diffusion dataset and the areas in the red rectangle shape are those problematic areas I meant…

I think the areas you’re highlighting are where you’d expect strong susceptibility-induced distortions, due to field inhomogeneities. These will always be problematic areas to image, especially at high resolution. The strategy for the HCP was to acquire the data twice with reversed phase-encoding direction, running left-right / right-left (which is unusual, most people use anterior-posterior), and use FSL’s topup & eddy tools to try to correct for these distortions – but as you can clearly see, in some regions it’s not possible to recover the signal accurately. I don’t think there’s very much that can be done here, unfortunately…