Assistance needed in using Allen 3D atlas to merge with PET CT

Technical
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Good day!

I have downloaded average_template_50.nii and want to merge it with PET CT file in 3D slicer or any similar software related to Radiology and neuroscience. The issue I am facing is that it seems the size of atlas or coordination doesnt change with different registeration methods. I like to keep my CT as fixed volume which is already matched with PET and use the atlas as moving volume to merge roughly with mouse brain. I see methodology frequently being used in literature however I dont have a very detailed step by step guide if sb doing this routinely or has a manual please share it will save the day Best SP

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Thanks for your question. Generally, we use ANTs for registering to/from the mouse template (see: Registration — ANTsPy release stable documentation). However, the registration transforms may not be applicable if your PET CT file is novel (ie. not already curated by the Allen Institute).

Could you provide more information about the PET CT file (voxel size, origin, provenance)?

Best,

Ashwin

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thanks for the info I acquired it on a new mediso I will check this info

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