[Mrtrix-discussion] streamtrack and FA cutoff

[Fabrizio Fasano]

Thanks Donald,

our problem is that the tracks I described above go through regions where white matter is missing, 

what do you think about using a white matter mask instead of an FA derived one?

in this case  I would use a WM mask obtained by a well registered (to DTI) and well segmented T1w volume, 
for example by using ANTS with multivariate registration T1w->FA and T1w->b0 

fabrizio

On Sep 20, 2011, at 10:42 AM, Donald Tournier wrote:

> 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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