It just tests whether the mask is zero or not, and treats it as binary.
Cheers.
On 22 Aug 2007, at 21:22, Michelle Voss wrote:
> hi all,
>
> I got different values when i used the call above on pve maps with
> a binarized vs. non-binarized roi...
> in avwstats++ with the -k option, does it weight the image with the
> mask or do the min and max intensities in the mask act as a min and
> max threshold for pulling out pve's ?
>
> thanks,
> Michelle
>
>
>
> On 6/28/07, Jiansong Xu <[log in to unmask]> wrote: Thanks.
>
>
> > From: Matt <[log in to unmask]>
> > Organization: ma-tea.com
> > Reply-To: FSL - FMRIB's Software Library < [log in to unmask]>
> > Date: Thu, 28 Jun 2007 08:28:26 -0400
> > To: <[log in to unmask]>
> > Subject: Re: [FSL] volume of gray matter within a ROI
> >
> > 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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---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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