Hi.
> 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
> milliliter?
>
> 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
this; http://www.fmrib.ox.ac.uk/fslfaq/#fast_volume
Cheers.
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
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