user-forum > RE: Stereotaxic coordinates
Mar 12, 2020  11:03 AM | Eszter Agnes Papp
RE: Stereotaxic coordinates
Dear Marc,

I have done a landmark-based affine registration between the Waxholm Space T2*-weighted MRI template and the high resolution rat skull CT provided by the DigiMorph Library at, and found the following voxel coordinates for the interaural line:

IAL Right: CT(792,546,1298) WHS(447,331,609)
IAL Left: CT(189,515,1291) WHS(34,324,626)

Please note that this is based on a linear transformation between the two volumes, with its limitations regarding precision. Also, some differences may exist between animals (no strain is specified on DigiMorph). Still, I hope that it gives you a starting point.

We plan to export the transformed version of the CT and share it here on NITRC, but this will take some time as currently we have a lockdown at the university due to COVID-19. It may be faster to take the CT yourself and work with it further, eventually create a non-linear alignment. If you do so, it would be great if you could share the end result as this would be helpful for many people.

All the best,

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Marc Lalancette Mar 2, 2020
Eszter Agnes Papp Mar 5, 2020
Marc Lalancette Mar 5, 2020
RE: Stereotaxic coordinates
Eszter Agnes Papp Mar 12, 2020
Marc Lalancette Mar 12, 2020