Dear Amir,

> I have segmented 750 T1 scans of 1.5T scanners, using the “New Segment”,
> SPM8. This is a volumetric study.
>
> I am going to count the number of GM and WM voxels to calculate regional
> brain volume. But it seems to me that I should perform a thresholding on the
> GM and WM images, since visually I can say some non-zero voxels can never be
> brain tissue. On the other hand, some voxels are regarded both as GM and WM.
>
> I have tried several thresholds, starting from 5% to 70%, but to me and just
> visually 20% seemed the best. I just wanted please to ask you if you know
> any certain level for this thresholding? My results of regional brain volume
> seem dependant on this threshold level, and although the changes are not
> very significant, since I have collected data from 3 different scanners it
> becomes more important for me.

I would be cautious about voxel counting using thresholded images.  In
doing so, if you use a threshold of 0.2 (20%), you would be treading a
voxel with a value of 0.21 the same as a voxel with a value of 0.99,
when in fact these very likely contain different amounts of gray
matter.  The continuous nature of the segmented images reflect, among
other things, partial volume effects, and so I would think it would be
more accurate to assume that the first voxel in my example was about
21% gray matter and the second 99% gray matter, which will indeed give
you a different result when you count up the volume.

The most common way to calculate volume of a tissue class is to
integrate over all voxels, and then take into account voxel size, to
provide a meaningful number.  See, for example, Ged Ridgway's very
helpful get_totals.m script:

http://www.cs.ucl.ac.uk/staff/G.Ridgway/vbm/get_totals.m


Hope this helps!

Best regards,
Jonathan

-- 
Dr. Jonathan Peelle
Department of Neurology
University of Pennsylvania
3 West Gates
3400 Spruce Street
Philadelphia, PA 19104
USA
http://jonathanpeelle.net/