yes - that's right - I didn't comment on that - but these options are
I think over-rided by the -k masking option..I think.
Cheers.
On 16 Oct 2007, at 16:21, Ged Ridgway wrote:
> 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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Stephen M. Smith, Professor of Biomedical Engineering
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