[Mrtrix-discussion] ROI options

[J-Donald Tournier]

Hi Ayca,

It's difficult to figure out what the problem from so little information -
it would be better if you could provide the commands used, and any output
from them. However, from what you say I think the most likely issue is that
you've tried to use an image of atlas labels as an ROI in MRtrix? I don't
think converting from nii to mif is going to make any difference here, the
main issue is that streamtrack (or tckgen if you're using MRtrix3) expects
each -seed, -include, -exclude or -mask image to be a binary ROI - it
should only correspond to a single structure. The atlas-supplied ROIs are
most likely integer images with different values for each structure. So it
would be useless as a seed or include region, you need to extract the
particular index you're interested in. I don't think there's a neat way to
do this in MRtrix 0.2, but in MRtrix3, this would be a simple matter of
"mrmath atlas.nii 4 -eq roi4.nii" to extract index 4 for example.

Apologies if that's not the problem - in that case, please post as much
information as you can to help us figure out the issue.

Cheers,
Donald.


On 16 October 2015 at 22:57, Ayça Altınkaya <ayca.altinkaya at gmail.com>
wrote:

> Hi,
>
>
> I want to use some anatomical structures from known atlases as ROI. I
> converted individual structure files from nii to mif. And tried to use the
> file’s path as seed or include ROI.
>
> Program seems to be run and calculate a tract. But when I display the
> tract and ROI together, I never see the ROI. And tract seems doesn’t use my
> structure file.
>
>
> Could you please help me?
>
>
> Thank you,
>
>
> Ayca
>
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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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