Hello Everyone,
I need urgent help!!!
I am trying to register one pig brain atlas space to another atlas space so that I can transform white matter (WM) and CSF masks from one atlas to the other. I attempted this using antsRegistrationSyN, and while the outer brain contour appears to align reasonably well, the internal brain structures do not align properly at all. I am unsure how to proceed and would appreciate guidance on the best approach to handle this situation.
Thanks
Sanjida
Are you able to share the data? It’s hard to tell what’s going on from the description alone
AFNI has been used several times in the past for various pig studies. In AFNI, you could use @animal_warper for alignment between two templates and move the ROIs from atlases between them. Cost functions for the alignment need to be appropriate for the types of templates. If the templates are similar modalities, you would likely use a cost function like lpa or lpa+ZZ. If they are different (e.g. T1 vs T2), you might use lpc or lpc+ZZ. If the datasets are very smooth, then an nmi cost function might be appropriate.
https://www.sciencedirect.com/science/article/pii/S1053811921002925