AAL3 in MNI_N27 to MNI152

AFNI Message Board
1

Dear AFNI experts,

I am currently using the AAL3 (aal) parcellation for my fMRI analyses. The challenge is that all my data has been preprocessed in MNI152NLin2009cAsym template space, but AAL3 is in MNI_N27.

What is the best solution to convert AAL3 into MNI152 template space? Are there affine transforms somewhere that I could use or does simply resampling do the trick?

Looking forward to your response.

2

An affine transformation won't be very effective because the two spaces are close to the same. There are a few choices:

  1. Resample and ignore differences between the two template spaces. Probably what most do.
  2. Use the N27 template instead. A completely reasonable choice. I think the 2009c will probably be a better target, and give more consistent correspondence across subjects.
  3. Nonlinear alignment of N27 to 2009c. A single 3dQwarp command can compute the warp, and then apply the warp to the atlas. Easy to try and effectively moves regions limited by the nearest neighbor interpolation. You can repair regions with "modal smoothing".
  4. Resample as in 1 but only fill cortical ribbon of MNI 2009c (determined by FreeSurfer) using @ROI_modal_grow.
  5. Project to surface of N27 (3dVol2Surf) and reproject from surface to volume (3dSurf2Vol) of 2009c, again using @ROI_modal_grow.

I have done 3, 5 before for other atlases, but it's up to you.

1 Like