[Mrtrix-discussion] streamtrack and FA cutoff

[Donald Tournier]

Hi Fabrizio,

You might find your question has already been partly answered here:
http://www.nitrc.org/pipermail/mrtrix-discussion/2011-May/000207.html

This is the relevant section:

*For both SD_ methods, the cutoff actually refers to the FOD amplitude in
the direction of tracking - FA is NEVER considered for these tracking
methods. *

If you truly want the tracking to stop based on FA, you could threshold the
FA map at your desired level and use the resulting mask with streamtrack and
the -mask option. I wouldn't recommend this though, the whole point of
MRtrix and CSD is to avoid using tensor-derived measures since they are
hopelessly inadequate in crossing fibre regions...

Cheers,

Donald.


On 20 September 2011 18:30, Fabrizio Fasano <hank7v at gmail.com> wrote:

> Dear all,
>
> I used the following command
>
> >streamtrack SD_PROB CSD10.mif -seed ROIseed.nii  -include ROItarget.nii
> -mask mask.mif -num 100 -maxnum 100000 seed2target.tck
>
> and the resulting tracks in mrview go through regions with very low FA
> (0.03, 0.07, etc) when it was expected a cutoff of FA>0.1, the same happened
> when I directly used the option -cutoff 0.1
> NB. in mrview I didn't use a slice thickness (crop to slab) 2.0 and my
> slice thickness is 1.5mm
>
> any suggestion to be sure to force the procressing to stop if FA>0.1?
>
> thank you a lot,
>
> fabrizio
>
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>


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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