Hi Guang,
it's hard to tell without looking at the surfaces. I don't think a wm mask will help. You could try using the expert options to change the intensity bounds that are automatically detected by mri_segment and mris_make_surfaces.
cheers Bruce On Mon, 29 Mar 2010, Guang Zeng wrote:
Hi there,
Recently, I use FreeSurfer analyze a clinic data, the result show a very thin cortex layer, (see figure. 1). I load the wm,mgz (see figure.2), and then overlay the segmentation results, (see figure. 3). As you can see, part of wm.mgz around the wm mask boundary are classified as gm, I guess this is because of partial volume.
My question is if I use a better wm mask to replace freesurefer's brainmask (see figure. 4), could I get a better result?
Thanks! Guang
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