[Mrtrix-discussion] generate ROI 3D using gen_ROI in a script

[Donald Tournier]

Hi Arnaud,

gen_ROI will create a binary mask image with ones only within the
boundaries specified with the -coord option. These are passed as voxel
indices (as a number sequence, e.g. -coord 0 10:20 for indices 10 to 20
along the x-axis). It looks like you need them to be specified in scanner
coordinates, so this might not be suitable for you. Also, it can only
generate rectangular regions, which may or may not be suitable for you. If
you can convert the position and size to voxel coordinates, then it will do
what you want, but otherwise it would require a bit of effort to code
something up.

Hope that helps.
Cheers,

Donald.



On 30 September 2013 16:53, Arnaud Boré <arnaud.bore at gmail.com> wrote:

> Dear Mrtrix experts,
>
> I try to create a 3D ROI using its position and with a size of 10mm.
> I think that using gen_ROI I will be able to do it but so far I didn't
> find how.
>
> Can you help me please.
>
> Thank you
>
> Arnaud
>
> --
> Arnaud BORE
> Research assistant
> Cellulaire : (001) 514-647-8649
>
>
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>


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

*Senior Lecturer, **Biomedical Engineering*
*Division of Imaging Sciences & Biomedical Engineering
King's College London*
*
*
*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH
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