Allen mouse brain CCF v3

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1

Hi,

I have been trying to register some mouse brain images to the Allen Mouse Brain Common Coordinate Framework v3 brain template.
I started by converting the NRRD format to NII using the 3dSlicer software.
After that, I downsampled the Allen CCF to 75 micrometers to match our data using the 3dresample function.
Then, I tried aligning the centers of the images but the @Align_Centers function did not work.
I also tried using 3dAllineate for linear registration and auto_warp.py for non-linear registration but none of them worked.
Same steps have worked before on the template from this link:
http://www.mouseimaging.ca/technologies/mouse_atlas/C57Bl6j_mouse_atlas.html
But I didn’t have luck using the Allen mouse brain.

Would you please let me know what I need to do to make it work?"

2

Check the units of the Allen mouse resampled from NRRD format. The last time I looked, Slicer conversion was off by a factor 1000, i.e. microns instead of the mm units that are usually recorded in a NIFTI dataset. Also take a look at our version here:

https://afni.nimh.nih.gov/pub/dist/atlases/mouse/