[Mrtrix-discussion] help with streamtrack

[Thijs Dhollander]

Hi Gabriel,

Your tracks are seeded (i.e. started) from a seed region, and they are constrained to stay in the mask (i.e. they stop -but are not discarded- if they bump into the edge of your mask).  So if I understand your goal right (you want to perform a "within-ROI-tractography"), you'd want to set your ROI as both your seed and mask region.
Using the full brain as a seed and the ROI (which is a sub-region of the brain, I suppose) as mask, makes no sense (even though the results will be the same): no tracks will start from the full brain, outside the ROI, anyway; as they are already outside your mask.

In conclusion, it's of no use to seed in regions that are not at least contained within the mask.

Hope this helps! :-)

Greetings,
Thijs


Thijs Dhollander
PhD Student

thijs.dhollander at uz.kuleuven.ac.be
tel. +32 16 34 90 37
gsm. +32 475 36 44 27

Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)
Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus 7003 | B-3000 Leuven | http://www.medicalimagingcenter.be

From: mrtrix-discussion-bounces at public.nitrc.org [mailto:mrtrix-discussion-bounces at public.nitrc.org] On Behalf Of Gabriel Gonzalez Escamilla
Sent: vrijdag 21 oktober 2011 17:40
To: mrtrix-discussion at public.nitrc.org; mrtrix-discussion at public.nitrc.org
Subject: [Mrtrix-discussion] help with streamtrack

Hello dear mrtrix experts and users, I'm new in usin this excellent tool.

And as I'm new with it, I have a doubt, which I guess is not so complicated to you,

 I'm wondering which would be the best way to perform the streamtrack for a within ROI tractography. I'd look at the options, an saw that I can use a seed region and a mask region for this proposal, as describeed in the documentation I know that must use the -mask option but wondering if I should use the same ROI as seed region, or should enter the entire brain mask?.

Any help will be appreciated

Thanks in advanced,
Gabriel

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