Can masks created by SPM be used by AFNI

Hi AFNI gurus,

I have to use some mask.nii created by SPM for the beta maps created by AFNI. When I use 3dinfo mask.nii, it shows mask.nii is in ORIG space. I do know that these mask.nii are in MNI space. My thought is, as long as they are in the same common space, I should be fine. Can I just align my stats.nii from to TT_EPI.nii template?

Thank you as always!



You should be able to use NIFTI datasets from any source, including SPM. For convenience, you may want to relabel the space with “3drefit -space MNI mask.nii” or use nifti_tool to set the sform_code and qform_code to 3 (NIFTI_XFORM_MNI_152).

You can try to use them, but please make sure that the masks are properly aligned with the MNI template brain when you view them in AFNI. Otherwise, bad things will happen.