Hi Tamara,
Possibly I need another cup of coffee, but why the "-l 1 -u 1"? If you
were looking at the discrete segmentation image (CSF=0, GM=1, WM=2)
then I can see why this would be needed, but if you're looking at
separate partial volume esimate images from fast -ov then don't you
just want to integrate these over the hippocampal mask? E.g. multiply
the value from `fslstats pve_X -k hippo-mask -m` by the number of
non-zero voxels in the hippo-mask, from e.g. `fslstats hippo-mask -V`,
and then multiply this by the *original* volume of your rat-image
voxels in cubic mm.
Best,
Ged.
> After FAST I get the pve files for each tissue (prest1_pve_1=GM,
> rest1_pve_2=WM and rest1_pve_0=CSF)
[...]
> fslstats rest1_pve_1 -l 1 -u 1 -k hippo-mask -m
> 0.913644
> fslstats rest1_pve_1 -l 1 -u 1 -k hippo-mask -v
> 6873 12161.580241
> I do the same for WM rest1_pve_2 (l=2 and u=2) and for CSF rest1_pve_0 (l=0,
> u=0).
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