AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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mabbasi6
August 13, 2020 02:38PM
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:
[www.mouseimaging.ca]
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?"
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Allen mouse brain CCF v3

mabbasi6 August 13, 2020 02:38PM

Re: Allen mouse brain CCF v3

Daniel Glen August 13, 2020 02:54PM