> BET with -c did help to get rid of some non-brain matters below the brain.
> After running FAST with "Binary segmentation :One image per class" selected,
> I get 3 sets of image: image_0.hdr, image_1.hdr, and image_2.hdr.
> image_0 should be CSF
> image_1 should be Grey matter
> image_2 should be white matter
> Is this correct?
yes, that's right.
> Another question is, when I do "avwstats image_0.hdr -v", what is the second
> number that is displayed? Is that total CSF volume? if it is, what is the
> UNIT? Usually, i get values like 465223.234.
> If I'm wrong, how do you get total volume of CSF (or anyother matters) in
> In our cases, seems like segmented CSF is quite large, at least larger than
> grey or white matter. I don't think this is true. Is there a justification
> that i can make to correct this?
yes - if you just type "avwstats" you see the usage list. -v gives voxel
count and volume (same units as the header) for the _whole image_.
However, you are probably wanting the volume of CSF - see the FAQ for
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve