Or I completely misunderstand you and it's the raw data plus the GM TPM to illustrate the raw data having a similar orientation after manual adjustments, with the segmentation output still not satisfying?
In that case the deviance might still be too large, the raw data would be around 10 to 15 mm "too high" along z, so you would have to shift the raw file downward = shift the origin upward.
If this doesn't solve the issue, please send the raw file (compressed as RAR or ZIP) or a download link to me, I'll check the file tonight.
Best
Helmut
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