Hi SPM experts,
It's the first time I got some mouse data to work on. Until now I only worked with human brains.
I've used the spmmouse toolbox for SPM 8 to segment the data. And I calculated a first statistical test with them. So far everything seems to work fine.
But then I feel a bit lost because I don't know how to lable the results properly with a matching atlas.
In the paper of Steve Sawiak et al. (2009) they mention the Paxinos and Franklin atlas to look up the bregma coordinates. Do you know if the coordinates in the SPM output are bregma coordinates when I use SPMMouse? Or do I have to transform them first?
The Paxinos and Franklin atlas can only be used if I want to look up coordinates. But what would I do, if I need a mask for a certain brain region?
What atlas do you use to lable the significant blobs and extract digital masks for brain regions from?
I would be very grateful for any hint or comment.
Thank you!
Best, Katharina
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