Hi, 

I tried the W2MHS software and in general am very satisfied by the resulting white matter hyperintensity maps. 
I use thresholded versions of the pmap as masks for quantitative parameter maps.
One my goals is to make the distinction between periventricular lesions and lesions in deep white matter. For this purpose I derived a 'periventricular area' by inflating the ventricle mask (Vent_bin*.nii) and subtracting this from the original ventricle mask. However, the ventricle mask (Vent_bin*.nii) sometimes appears truncated and lower regions of the ventricle are excluded (this happens in the region growing part of the code: 'Constructing PV Estimates and Ventricle template'). The result is that my periventricular area is not very representative.

Is this a known issue? And would there be ways to improve the ventricle delineation?

I tried to do this by playing with some settings in the 'Constructing PV estimates and Ventricle Template' section, yet could not get a more complete ventricle mask without also obtaining CSF outside the ventricles.
I also tried the ALVIN lateral ventricle segmentation (which uses a predefined ventricle template). This way I obtained a lateral ventricle segmentation that includes the lower regions of the ventricles, but some other regions were excluded (probably because of the fact a template is used).

I attach an image of the ventricles as delineated by W2MHS and ALVIN to illustrate the issue.

Kind regards,

Thibo