How to go from MNI2009b to MNI152NLin2009cAsym


I have an atlas parcellation (in MNI2009b ) I would like to apply to my (which is in MNI152NLin2009cAsym). Is there a database with the relevant transformation matrix that one can use for these situations?

Or is it the case that a, b and c just differ in sampling and if I want to go from “b” to “c” I can just downsample to 1mm from 0.5mm?

Hi @foldes.andrei,

You can find the T1s for those templates with TemplateFlow and calculate the registration with those. GitHub - templateflow/templateflow: The TemplateFlow Archive - A DataLad super-dataset


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Right! So I download my the T1w images of interest and run something like?

antsRegistration -d 3 \
                 -r [MNI152NLin2009bSym_T1w.nii, MNI152NLin2009cSym_T1w.nii, 1] \
                 -m Mattes[MNI152NLin2009bSym_T1w.nii, MNI152NLin2009cSym_T1w.nii, 1, 32, Regular, 0.3] \
                 -t Affine[0.1] \
                 -c [1000x500x250x100,1e-6,10] \
                 -s 4x2x1x0vox \
                 -f 6x4x2x1 \
                 -l 1 \
                 -o [output_prefix_, output_warped_image.nii, output_inverse_warped_image.nii]

So then I take matrix stored output_prefix_ and use ants to apply the transformation?

antsApplyTransforms -d 3 \
                    -i parcellation_image.nii \
                    -r MNI152NLin2009cSym_T1w.nii \
                    -o transformed_parcellation_image.nii \
                    -n NearestNeighbor \
                    -t output_prefix_Affine.txt

Can’t say for sure, I am not a big ANTs CLI user (or understander), but if it works and looks good, then great!