Yes, indeed: calculations on fdt_paths should be done by avwmaths_32R.
Cheers-
Andreas
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Stephen Smith
Gesendet: Mittwoch, 30. November 2005 10:39
An: [log in to unmask]
Betreff: Re: [FSL] Calculating FA after probabilistic tractography
Yup - though I suspect that the "pathway" image is of integer type, so this would fail to keep the FA values - hence replace the first 'avwmaths"
with "avwmaths_32R" ?
Cheers.
On Wed, 30 Nov 2005, Tim Behrens wrote:
> Hi Kristen.
>
> > 1) I am interested in calculating probabilistic tractography between
> > two anatomically identified regions. I created two masks, one for
> > each ROI, and Probtrack is currently running overnight (hopefully
> > without errors!). I used the "Symmetric - Two Masks" option. Is
> > this the correct option to use for this purpose?
>
> Sounds fine.
>
> >
> > 2) Afterwards, I am interested in calculating the FA of the tract
> > identified using Probtrack that is above a certain probability
> > threshold. Is there a way to do this in FDT?
>
> yep - just use avwmaths.
>
> avwmaths pathway -thr <threshold> -bin -mul dti_FA FAmas #will output
> an image of the FA in the pathway, then e.g.
> avwstats FAmas -M
> #will give you the mean value.
>
> Cheers
>
> T
>
>
> >
> >
> >
> > Thanks for your help!
> >
> >
> >
> > Kristen
> >
> >
>
>
--
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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