[Mrtrix-discussion] RE: mask ROI

[Patai, Zita]

Dear Thijs

Thank you for the quick response!

I understand what you have said, and it makes sense. Do you recommend either option as being more 'anatomically' correct?
What is interesting is that with option b, I got a better tract, even though as you say more streamlines may have stayed in there...

Thanks again!
z

From: mrtrix-discussion-bounces at www.nitrc.org [mailto:mrtrix-discussion-bounces at www.nitrc.org] On Behalf Of Thijs Dhollander
Sent: 22 May 2013 20:57
To: mrtrix-discussion at www.nitrc.org
Subject: [Mrtrix-discussion] RE: mask ROI

Hi Zita,

There is in fact a difference between both scenarios: tracks which enter an exclusion ROI are entirely discarded, while tracks which leave a mask are just stopped (but not discarded if they meet the other requirements, e.g. the minimum track length, at that point).
Qualitatively, in the final distribution of accepted tracks, you are thus likely to see (a lot) less tracks ending "on" (i.e. very near) the boundary of the exclusion ROIs in scenario (a), as opposed to scenario (b).  Also, scenario (a) will take longer to obtain an equal amount of accepted tracks, as opposed to scenario (b).

Cheers,
Thijs

Thijs Dhollander
PhD Student

thijs.dhollander at uzleuven.be<mailto:thijs.dhollander at uzleuven.be>
tel. +32 16 34 90 37
gsm. +32 475 36 44 27

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

From: mrtrix-discussion-bounces at public.nitrc.org<mailto:mrtrix-discussion-bounces at public.nitrc.org> [mailto:mrtrix-discussion-bounces at public.nitrc.org] On Behalf Of Patai, Zita
Sent: Wednesday, May 22, 2013 21:39
To: mrtrix-discussion at www.nitrc.org<mailto:mrtrix-discussion at www.nitrc.org>
Subject: [Mrtrix-discussion] mask ROI

Dear MrTrixers

Just checking that there is no difference in the 'quality' or 'number of streamlines' generated if I do

a)      a mask of whole brain but include many exclusion ROIs

or

b)      a mask ROI which is smaller than the whole brain and is already excluding those regions which I did as -exclude above
?

Many thanks!
zita
_________________________
Eva Zita Patai
Postdoctoral Research Associate
UCL, Institute of Child Health
e.patai at ucl.ac.uk<mailto:e.patai at ucl.ac.uk>
020 7905 2730

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