[Mrtrix-discussion] How to generate fibers that end near the GM

[J-Donald Tournier]

Hi David,

I don't think there's any way of doing what you're trying to achieve in
MRtrix 0.2.x - MRtrix3 on the other hand includes the whole ACT framework
<http://www.ncbi.nlm.nih.gov/pubmed/22705374>, which is designed for this,
amongst other things.

Cheers,
Donald.


On 5 December 2014 at 10:13, Romascano David <david.romascano at epfl.ch>
wrote:

>  Hi everyone,
>
>
>
> I’m trying to generate 100'000 fibers that start and end near the GM, and
> seeding randomly from the WM.
>
>
>
> Following this post (
> www.nitrc.org/pipermail/mrtrix-discussion/2011-October/000289.html), I
> manage to create tracks that connect the left thalamus with the left cortex
> for example, by running the following command:
>
>
>
> streamtrack -seed WM_mask.nii -mask WM_mask.nii -include
> R_thalamus_mask.nii -include R_cortex_mask.nii -number 10000 -maxnum 100000
> -minlength 10 -step 1 -nomaskinterp -stop SD_PROB FODsh.mif fibers.tck
>
>
>
> I then tried to generate fibers that start and end near the GM. To filter
> tracks that end near the GM, I dilated my GM mask and set it twice as an
> inclusion ROI in the command:
>
>
>
> streamtrack -seed WM_mask.nii -mask WM_mask.nii -include GM_dil_mask.nii
> -include GM_dil_mask.nii -number 10000 -maxnum 100000 -minlength 10 -step 1
> -nomaskinterp -stop SD_PROB FODsh.mif fibers.tck
>
>
>
> But then some of the selected fibers end inside the WM… Assigning them to
> the nearest GM region doesn’t seem realistic.
>
>
>
> I tried to run using ‘-include ROI1.nii –include ROI2.nii’ where ROI1 and
> ROI2 are both copies of the GM_dil_mask, but it didn’t change the output.
> Running the command without the “-mask” option didn’t help either.
>
>
>
> I thought about running streamtrack separately for each of the GM dilated
> regions, using ROI1 = the corresponding dilated GM region and ROI2 = all
> other dilated regions, and then concatenate all the track files, but this
> would bias the tracking because of the different sizes of the GM regions
> right ?
>
>
>
> Does anyone have an idea on how I could proceed ?
>
>
>
> Thanks in advance and best regards,
>
> David Romascano
>
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>
>


-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*


*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
*W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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