Dear AFNI experts,

I would like to register some ROIs in the MNI space to the T1-space of one participant.

I used auto_warp.py to to extract the transformation T1-2-MNI space and then use 3dNwarpApply to apply the inverse transformation to my ROIs. While the direct transformation looks fine (t1 to MNI), when I apply the inverse transformation my ROIs are not correctly registered. Could you please give me some advice on that?

these are the commands:

auto_warp.py -base MNI152_T1_2mm_brain.nii.gz -input PT4_T1_3D_AX_brain.nii -qblur 1 3 -unifize_input yes -save_script script -skull_strip_base no -skull_strip_input no

3dNwarpApply -master anat.nii -source LEFT_IFG44.nii -iwarp -nwarp ‘anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D’ -interp NN -prefix test_roi_left_IFG.nii



Hmmm … I’d like to look at this. Can you make the data files (and instructions) available to me on Dropbox or some other site?
You can send me a private message on this forum when it is ready, if you are going to do so.

thank you very much for your response. i will definitely do that.


I’m looking at the data now. Will try to understand what’s going on.

I have some results for you, based on the datasets you provided. Please check your email.

Long story made short: use the @SSwarper script, not auto_warp.py, to take human brain images to MNI space. In particular, using the nonlinearly aligned MNI template gives more accurate results than the older linearly aligned template.