Hi AFNI experts,
I am running into an issue for applying some transforms. I have a T1 brain which I have rigidly aligned to my EPI scan (tx_1.1D) with the cmass flag in 3dAllineate. I have that same T1 brain also rigidly aligned to the MNI template for AC-PC alignment (tx_2.1D) using -cmass. I use cat_matvec to combine the transforms as follows:
cat_matvec tx_1.1D -I > tx_1_inv.1D
cat_matvec tx_1_inv.1D tx_2.1D > tx_EPItoACPC.1D
If I apply this transform using 3dAllineate to the T1 image (aligned to EPI after tx_1) it looks correct for APCP alignment with MNI template:
3dAllineate -base tpl.nii -source T1toEPI.nii -1Dmatrix_apply tx_EPItoACPC.1D
When I apply the same transform to the EPI scan it looks fairly shifted in the saggital plane by 15mm or so and also below the template by several millimeters.
- Does the matrix coming from 3dAllineate take into account the initial cmass operation?
- Could any of this be related to the fact that my T1 is 0.8mm iso while the EPI resolution is 2mm iso?
I also tried a few things with 3dNwarpApply
3dNwarpApply -nwarp ‘IDENT(EPI.nii) tx_EPItoACPC.1D’
3dNwarpApply -nwarp ‘IDENT(EPI.nii) tx_1_inv.1D IDENT(T1.brain.nii) tx_2.1D’
and a few other combinations but no success.
If I run it in two stages it works fine:
3dAllineate -1Dmatrix_apply tx_1_inv.1D -source EPI.nii -base T1.brain.nii -prefix temp1.nii
3dAllineate -1Dmatrix_apply tx_2.1D -source temp1.nii -base tpl.nii -prefix EPItotpl.nii
Any help for how to concatenate the warps properly would be appreciated.