[Mrtrix-discussion] questions about streamtrack command

[Donald Tournier]

Hi Marina,

Yes, that's correct, unless you use the -fraction option, in which case it
will be that number divided by the number of tracts in the file.

Cheers,

Donald

On 29 May 2012 17:37, Curci Marina Carmela <marina.curci at epfl.ch> wrote:

> I thank you for the information!!
>
> I have another question about the command tracks2prob: is the value of
> each voxel the number of tracks crossing that voxel?
>
> Thank you,
> Marina
> ________________________________________
> Inizio: Donald Tournier [d.tournier at brain.org.au]
> Inviato: giovedì 24 maggio 2012 2.40
> Fine: Curci Marina Carmela
> Cc: mrtrix-discussion at www.nitrc.org
> Oggetto: Re: [Mrtrix-discussion] questions about streamtrack command
>
> Hi Marina,
>
> How the command streamtrack choose the seed point?
>
> Seed points are generated at random by uniform sampling from the mask. The
> mask is defined as any location in 3D space where the image intensity after
> interpolation is greater than 0.5. You can disable the mask interpolation
> step with the -nomaskinterp option, so that seeds are only placed strictly
> within the voxels of interest. Unfortunately there is no option currently
> to ensure regular seed placement.
>
> Morever, while the command is running, I notice that there are generated
> streamlines but only some of them are selected, and the number of selected
> streamlines corresponds to the value given at the -number parameter.
> Which is the criterium by which streamlines are selected?
>
> Streamlines are selected if they satisfy all constraints. By default,
> there is a minimum length constraint, which I guess is the only reason you
> would currently get different numbers of generated vs. selected tracks. You
> can change that using the -minlength option. In general, additional
> constraints can be placed using the -include & -exclude options.
>
> Is there an option to set the number of generated streamlines instead of
> the number of selected ones?
> I've tried to run the command without any options but the numbers of
> generated tracks and selected ones do not match.
>
> There is no explicit option, but same result can be achieved very easily
> by setting -maxnum and -number to the same value (by default, maxnum is
> 100xnumber).
>
>
> My aim is to have a certain number N of tracks beginning from each seed
> point (voxel with intensity equal to 1) of the mask.
>
> This is a common request, but it's still not possible to do very easily.
> If the number of streamlines generated is large, you can certainly set the
> number of tracks to num_voxels x num_tracks_per_voxels, and get a very good
> approximation to uniform sampling of your ROI (you can find out the number
> of voxels in the ROI using the mrstats command). If you need to save the
> tracking results for each voxel separately, then you'll need to break up
> your ROI into individual voxel ROIs, and launch one streamtrack command per
> voxel. This can easily be done with a bit of scripting, but there is no
> easy way within MRtrix to break up the ROI into individual voxel ROIs.
> Maybe this is something that I could provide, since it would be trivial to
> code up. I'll have a think about that...
>
> Hope that helps,
>
> Donald.
>
>
>
> Thank you for your helpfulness,
> Marina_______________________________________________
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>
>
>
> --
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9035 7033
>



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