mice cerebellum template

Hi AFNI experts and users.
Is there any template for mice? Such as cerebellum.

There is the Allen mouse brain atlas and template. You could download that from their site. Otherwise, I’ve configured the 2011/2014 version to work with AFNI. Here is a link for you to download the datasets for that. This includes a modally smoothed version of the atlas, so the segmentation is smoother out of the coronal histology slicing plane.


After you download these datasets, make the appropriate changes in your .afnirc file like this:

AFNI_TEMPLATE_SPACE_LIST = allen_waxholm_mouse
AFNI_ATLAS_COLORS = Allen_Waxholm_Mouse
AFNI_SUPP_ATLAS_DIR = /directory_where_you_put_this_atlas/allen_mouse_waxholm

The 2017 version from Allen, based on more than 600 mouse brains, could also be made available. I am waiting for Allen to assign a standard coordinate system.



Thank you for making the Allen mouse template available.
I have been warping some of my mice brain images to the CCF3, and the warp is working great (using either auto_warp or @animal_warper). However, the Allen template and the annotation have been taken to the Talairach space. Is there a way to take it out of talairach (to orig space)?

I have tried this function:
3drefit -view
to change the view to orig, but converting its output to NIFTI and then back to BRIK format shows +tlrc space again.


@animal_warper produces output datasets in both the original and the template space. The help and the animal_outs.txt file describe which files are available in the original, native space output:

Atlas aligned to Subject (Optional - only if atlas provided)
+ seg_in_mydset.nii.gz - atlas segmentation aligned to native scan

Template aligned_to Subject
+ template_in_mydset.nii.gz** - template (e.g. NMT,D99) aligned
  to native scan

Text description of output
+ animal_outs.txt - list of important datasets and transforms in
                    output directory