Hello,

Thanks for this atlas.  How would you convert to stereotaxic coordinates from WHS coordinates, or the other way around?  Bregma and lambda landmarks are provided, but I believe we would also need the interaural line to be able to do this.  I am unable to determine it on the T2* image.  (Note: I am not familiar with rat anatomy, I only searched online to find images and definitions of the coordinate systems.)

We used the atlas to build a head model that we will use for electrophysiology, but we will need to be able to align it with our sensors by measuring external landmarks.  (2 landmarks is not enough to align a 3d object.)

Any help is greatly appreciated.
Best,
Marc

Dear Marc,

The interaural line is not readily visible in our MRI template, since the bony structures give no signal, so they are invisible unless there is some soft tissue directly attached.

In order to give you a good estimate for the position of the interaural line in Waxholm Space, we are working on aligning a CT (from another animal) to the atlas. I'll get back to you in a couple of days (hopefully) with the results.

Best regards,
Eszter

That would be great!  I had the same idea, but did not find an appropriate image.  Having the skull image could also be useful for head modeling.  Thank you!

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 http://digimorph.org/specimens/Rattus_norvegicus/, 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,
Eszter

Thank you Eszter.  Your efforts are much appreciated.  This will be sufficient for us for now.  
Best,
Marc