[Mrtrix-discussion] question regarding some tracking parameters

[Donald Tournier]

 Hi Peter,

This is probably what you're looking for:

Tournier J, Calamante F, Connelly A (2012). MRtrix: Diffusion tractography
in crossing fiber regions. International Journal of Imaging Systems and
Technology 22: 53–66.

Cheers,

Donald.


On 1 August 2012 23:25, Peter Neher <p.neher at dkfz-heidelberg.de> wrote:

>  Hi Donald,
>
> thanks for your answers! Is there any publication or something else that
> describes your probabilistic tracking implementation in more detail?
>
> Best
> Peter
>
>
> On 08/01/2012 02:03 AM, Donald Tournier wrote:
>
> Hello again,
>
>  I have some questions regarding the parameters of streamtrack:
>>
>>    1. Should it basically be the same to use a 0.2 thresholded FA image
>>    as -mask input as to apply a -cutoff 0.2? Because it is not. There seem to
>>    be fibers present in low FA regions if  I use the -cutoff parameter. It
>>    does change something, but I am not sure what exactly :)
>>
>>  Not quite the same, as you found out. The -cutoff applies to the FA as
> computed after tri-linear interpolation of the raw DWIs to the current
> point. For the mask, the cutoff point is the 0.5 level after tri-linear
> interpolation (you can use nearest-neighbour interpolation if you need to
> using the -nomaskinterp option). That will lead to the FA=0.2 level being
> in a different position than the mask=0.5 level, and in many cases, tracks
> will traverse regions where the mask is zero, simply because they avoid
> those parts of the voxel where the FA is below 0.2 after interpolation.
>
>
>>
>>    1. How is the -num parameter applied internally? Don't you just seed
>>    in every voxel of the mask image?
>>
>>  Nope. Seed points are generated randomly and uniformly from within all
> seed regions, in continuous 3D space. Even within a single voxel, the seed
> points will be distributed uniformly within its volume, rather than all
> starting from the centre of it. Streamlines will be generated until the
> number specified has been reached, or the -maxnum number has been reached
> (by default, this is 100x num). If you need to make sure you use exactly N
> seed points, set both -num and -maxnum to N.
>
>
>>
>>    1. If I use the probabilistic version, how many times is the
>>    trajectory originating from one seed point sampled and how is the result
>>    combined into one final fiber?
>>
>>  Once. Every streamline starts from a fresh seed.
>
>  Cheers,
>
> Donald.
>
>
>
>>
>>
>> Thanks in advance!
>>
>> Peter
>>
>> --
>> Dipl.-Inform. Peter Neher
>> German Cancer Research Centre
>> (DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
>> Division of Medical and Biological Informatics
>> Im Neuenheimer Feld 280, D-69120 Heidelberg
>>
>> Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
>> E-Mail: p.neher at dkfz-heidelberg.de, Web: www.dkfz.de
>>
>> The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.
>>
>>
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>>
>
>
>  --
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9035 7033
>
>
> --
> Dipl.-Inform. Peter Neher
> German Cancer Research Centre
> (DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
> Division of Medical and Biological Informatics
> Im Neuenheimer Feld 280, D-69120 Heidelberg
>
> Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
> E-Mail: p.neher at dkfz-heidelberg.de, Web: www.dkfz.de
>
> The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.
>
>


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