Because you want to exclude values above and below 2. In reality, the only
other values in the hard segmentation file will be 0 for empty space, 1 for
CSF, and 3 for white matter. I don't actually remember if avwstats++ uses
an inclusive or exclusive threshold, so if using upper and lower values of 2
doesn't work, you could use 1.9 and 2.1 for the same effect.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Jiansong Xu
Sent: Wednesday, June 27, 2007 5:53 PM
To: [log in to unmask]
Subject: Re: [FSL] volume of gray matter within a ROI
Thanks. Why both lower and upper threshold are 2?
> From: Matt <[log in to unmask]>
> Organization: ma-tea.com
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
> Date: Tue, 26 Jun 2007 20:03:33 -0400
> To: <[log in to unmask]>
> Subject: Re: [FSL] volume of gray matter within a ROI
>
> You could:
>
> A) Segment a structural scan on which you drew the ROI into grey matter,
> white matter, and CSF using FAST.
> B) Use avwstats++ <hard segmentation output> -l 2 -u 2 -k <your ROI> -V to
> find the volume of grey matter (value is 2 from the segmentation) masked
by
> your ROI.
>
> Peace,
>
> Matt.
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Jiansong Xu
> Sent: Tuesday, June 26, 2007 7:25 PM
> To: [log in to unmask]
> Subject: [FSL] volume of gray matter within a ROI
>
> Dear Friend:
>
> I have defined a ROI and want to measure the volume of gray matter within
> this ROI. What is the procedure?
>
> Thanks a lot.
>
> Jiansong
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