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simple case: T1 to MNI mapping for both structure and pre registered fMRI

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stnava edited this page Jan 12, 2016 · 4 revisions

User asked how to:

"1) normalize a patient´s T1 (lets call it T1.nii) to the MNI template (lets call it MNI.nii) by obtaining a transformation/deformation matrix (lets call it T1_to_MNI)"

  • antsRegistrationSyN.sh -d 3 -f MNI.nii.gz -m T1.nii.gz -o XXX
    • i would recommend instead 2 stages of registration: T1 to customTemplate to MNI and then concatenating these via antsApplyTransforms

"2) applying the T1_to_MNI matrix to T1.nii "

  • antsApplyTransforms -d 3 -r MNI.nii.gz -i T1.nii.gz -e 0 -t XXX1Warp.nii.gz -t XXX0GenericAffine.mat -o out1.nii.gz -v 1

"3) applying the T1_to_MNI matrix to the fMRI.nii data from the same patient (that have already been pre-registered to the respective T1.nii) "

  • antsApplyTransforms -d 3 -r MNI.nii.gz -i fMRI.nii.gz -e 3 -t XXX1Warp.nii.gz -t XXX0GenericAffine.mat -o out2.nii.gz -v 1

see documentation for details, e.g. the links at the top of this page

Note: The -r option defines the output spacing. you can change its resolution ( not its physical space ) freely and get valid results. e.g. via ResampleImage

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