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Dear FreeSurfer experts:

I am working on a manual for my lab and I would like to clarify the two points below (to which I couldn’t find answers in the online FS content available):

  • When editing the wm.mgz fails, can control points (CPs) be used to correct pial errors cause by lesions (e.g., perivascular spaces, microbleeds, WMH). I understand the FS tutorial recommends against this, however at times it seems that only editing the wm.mgz will not be sufficient (Figure 1 below)

  • Should white matter voxels with 0 intensity in the wm.mgz (inside the white surface) be filled in, even when these voxels do not affect white matter surface segmentation whatsoever? (Figure 2 below).

  • Would the cerebral white matter volumetric data (wmparc.stats) be affected by these 0 intensity voxels?

Thanks so much for you help!
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSFHR/PARF Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon