Hi Rick,
thanks for your fast response!
I followed your advice and called 3dAllineate with the following command:
3dAllineate -prefix ROI_in_native_space -base native_image.nii -source atlas_ROI.nii -twopass -cost lpa -1Dmatrix_apply native_al_mat.aff12.1D -autoweight -cmass -twobest MAX
The good news is that the program worked. The bad news is that the ROI is far off from where it should be (see image attached).
Did I miss something here?
Bests,
Philipp
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