Registration question

AFNI Message Board
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Dear AFNI experts,

I have preprocessed fMRI data aligned to T1 and would like to perform the following steps.

  1. Calculate T1 to MNI non-linear registration matrix.
  2. Use transformation matrix from 1 to transform fMRI to T1 into MNI.
  3. Calculate the average MNI-transformed T1 image.

Could you please advise which AFNI commands need to be used for each step?

Best,
JW

AFNI version info (afni -ver): Precompiled binary linux_openmp_64: Jun 7 2024 (Version AFNI_24.1.17 'Publius Septimius Geta')

code text  # or delete if not needed
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  1. sswarper2 - to align T1 to MNI template and skullstrip (also @SSwarper, auto_warp.py, 3dQwarp, 3dAllineate-3dQwarp, @auto_tlrc-3dQwarp, align_epi_anat.py-3dQwarp)
  2. afni_proc.py - to align EPI data to T1 anat, to MNI. Use something like these options (from example 6b of the help) to provide the warp information and template. Provide the input skullstripped anatomical data with
            -copy_anat                Qwarp/anat_warped/anatSS.FT.nii        \
            -anat_has_skull           no                                     \
            -anat_follower            anat_w_skull anat FT/FT_anat+orig      \
            -tlrc_base                MNI152_2009_template_SSW.nii.gz        \
            -tlrc_NL_warp                                                    \
            -tlrc_NL_warped_dsets     Qwarp/anat_warped/anatQQ.FT.nii        \
                                      Qwarp/anat_warped/anatQQ.FT.aff12.1D   \
                                      Qwarp/anat_warped/anatQQ.FT_WARP.nii   \
  1. 3dMean - to average datasets in the same grid and template space across subjects (maybe with 3dUnifize or 3dLocalUnifize first)
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Thank you so much for the detailed instruction. It was really helpful!