Trying to Align T2 to T1, getting different outputs


After running this command:

align_epi_anat,py -anat t1_file.nii -epi t2_file.nii -epi2anat -anat_has_skull yes -epi_strip None -suffix _aligned -rigid_body -epi_base 0 -giant move

I’m getting this output:

I thought +tlrc output suggested that I was aligning my T2 file to a template. Since I’m aligning to a T1 file, I thought I was supposed to be getting +orig as the output. Does it matter?

Thank you!

It’s likely you have a NIFTI dataset with one of its fields marked in an ambiguous way. If the sform_code is 2, that can translate to either a dataset that is in native/ orig space or in a standard space. In AFNI, we append the “view” suffix +orig or +tlrc to tell which kind of data it is. You can either transform the data in the AFNI format to the +orig view with

3drefit -view orig t2_file_aligned+tlrc.

or you can set the AFNI environment variable to say how to handle this:

@AfniEnv -set AFNI_NIFTI_VIEW orig