Dear FreeSurfer Experts,


We are collecting a 0.9mm isotropic FSPGR sequence on a GE MR750 3T scanner. We're observing, in many subjects, a problem mentioned in previous posts to the list where the pial surface does not follow the cortex properly in the anterior temporal lobe region (and also in some frontal regions). The white matter surface generally looks very good. This is with the default options from recon-all in v5.3.

We've also tried running the following options, based on previous posts (expert options) and the release notes for version 5.2:

-norm2-b 20 -norm2-n 5

and

-norm2-b 20 -norm2-n 5 -3T

In general, there is a modest improvement in the medial temporal lobe pial surface in most subjects. A substantial/desired improvement is observed in only a few subjects. In general, there was no detrimental effect to either the white matter or pial surface when using these flags.

Based on older posts to the list, we've also tried using the following flags:

-mprage

and

-washu_mprage

The improvement to the pial surface is much more substantial in almost all subjects, to some extent with the -mprage flag, mostly with the -washu_mprage flag. However, this dramatic improvement in pial surface accuracy was accompanied by many major issues with the white surface in widespread areas across the brain. Also, some subjects fail to reconstruct fully due to large defects in the surfaces with this option in place (also something I've read about happening to people using the -washu otpion on the list).

A few questions:

Would you suggest we also try the options "-norm1-b" and "-norm1-n" in addition to the norm2 options? If so, any suggested starting values to try?

Alternatively, would it be sensible to try to use the white surface from the default pipeline and combine it with (or perhaps initialize) the pial surface from the -washu_mprage flag?

Do you have other suggestions for us to try?

Thank you for your time and help!

Sincerely,

Las