# how to get the position from mrtrix3？

**URL:** https://community.mrtrix.org/t/how-to-get-the-position-from-mrtrix3/4725
**Category:** Uncategorized
**Created:** [April 2, 2021, 9:16pm UTC](https://community.mrtrix.org/t/how-to-get-the-position-from-mrtrix3/4725 "2021-04-02T21:16:50Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![Lingyufan](https://community.mrtrix.org/user_avatar/community.mrtrix.org/lingyufan/32/3302_2.png) [@Lingyufan](https://community.mrtrix.org/u/Lingyufan)
#### Post date: [April 2, 2021, 9:16pm UTC](https://community.mrtrix.org/t/how-to-get-the-position-from-mrtrix3/4725/1 "2021-04-02T21:16:50Z")

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Hello Everyone, I just face a problem while deal with the voxel index to position, base on the command [mrinfo] -transform: the transformation from image coordinates [mm] to scanner / real world coordinates [mm]. so I follow the equation : (x, y, z )T = transform\_R \* (i, j ,k)T + transform\_T, where (x, y, z ) stand for the position and (i,j,k) stand for voxel index, transform\_R and transform\_T all from transform, but the result I calculate can’t fix with the result in mrtrix. Please correct me if I understand something wrong, or any other convenient way to get the position.  
thanks a lot!

 ![1](https://community.mrtrix.org/uploads/default/original/2X/8/8f0509ed7f8d97c70ee4a0d56962b2bcec7e68db.png)

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### Author: ![bjeurissen](https://community.mrtrix.org/user_avatar/community.mrtrix.org/bjeurissen/32/28_2.png) [@bjeurissen](https://community.mrtrix.org/u/bjeurissen)
#### Post date: [April 2, 2021, 9:25pm UTC](https://community.mrtrix.org/t/how-to-get-the-position-from-mrtrix3/4725/2 "2021-04-02T21:25:00Z")

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The relevant documentation can be found at [Images and other data — MRtrix3 3.0 documentation](https://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html#the-image-transfom).

What I think is missing in your equation is the voxel size, as explained in this excerpt from the page linked above:

> In _MRtrix3_, the transform shown always corresponds to the transformation from image coordinates _in millimeters_ to scanner coordinates _in millimeters_ - the voxel size is not taken into account, and the image axes are always normalised to unit amplitude. This may differ from other packages.

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### Author: ![maxpietsch](https://community.mrtrix.org/user_avatar/community.mrtrix.org/maxpietsch/32/25_2.png) [@maxpietsch](https://community.mrtrix.org/u/maxpietsch)
#### Post date: [April 6, 2021, 8:59am UTC](https://community.mrtrix.org/t/how-to-get-the-position-from-mrtrix3/4725/3 "2021-04-06T08:59:23Z")

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The first figure in [Registration, transformation, regridding: concepts](https://community.mrtrix.org/t/registration-transformation-regridding-concepts/3684) might be useful.

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### Author: ![Lingyufan](https://community.mrtrix.org/user_avatar/community.mrtrix.org/lingyufan/32/3302_2.png) [@Lingyufan](https://community.mrtrix.org/u/Lingyufan)
#### Post date: [July 14, 2021, 2:20am UTC](https://community.mrtrix.org/t/how-to-get-the-position-from-mrtrix3/4725/4 "2021-07-14T02:20:10Z")

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Sorry for taking so long to reply to you, your suggestions have helped me a lot, thank you.

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### Author: ![Lingyufan](https://community.mrtrix.org/user_avatar/community.mrtrix.org/lingyufan/32/3302_2.png) [@Lingyufan](https://community.mrtrix.org/u/Lingyufan)
#### Post date: [July 14, 2021, 2:20am UTC](https://community.mrtrix.org/t/how-to-get-the-position-from-mrtrix3/4725/5 "2021-07-14T02:20:53Z")

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Thank you for your suggestion, this wiki is very helpful!