Hi,
While using 5ttgen hsvs, we noticed that the brainstem is assigned to volume 4 (pathological tissue) with the hsvs algorithm, cf screenshot 1.
Although the 5ttgen hsvs algorithm includes the option to assign the brainstem to white matter, it is confusing to see the brainstem in the pathological tissue class.
Shouldn’t the brainstem always result in the same tissue class, regardless of the 5tt algorithm used, and especially not in vol. 4 (pathological tissue class)? Cf. screenshot 2 where I have used the 5ttgen freesurfer algorithm which maps the brainstem in vol. 2 and only the lesion in vol. 4.
Could someone please explain to me if this behaviour is intentional or a bug? Probably @rsmith knows more about this?
As always, thank you very much for your support.
screenshot 1
screenshot 2
