afni_proc.py volreg_tlrc_warp

AFNI Message Board
1

Hello AFNI team,

I would like to use a WARP in tlrc_NL_warped_dsets the has been created using 3dNwarpCat.
This WARP originated from multiple .1D and WARP files and works perfectly when used with 3dNwarpApply.

The problem is that if I only input 1 WARP (and the anat file) in volreg_tlrc_warp, it doesn’t work because volreg_tlrc_warp needs 3 files.
Can I add a .1D file with just 0?

Thank you for your help
Clément

2

Hi, Clément-

To be clear—I think “-volreg_tlrc_warp” takes no additional arguments, it is just a switch or flag.

When using @animal_warper or @SSwarper, you likely have the full warp in 2 pieces (an affine part in a *.aff12.1D file, and a nonlinear part, in a _WARP volumetric dset).

The afni_proc.py option “-tlrc_NL_warped_dsets” does require using 3 arguments after it: an anatomical datset, the affine *.aff12.1D file, and the warp _WARP dset. I don’t see a way to not provide all three.

  • If there is an *.aff12.1D file, I think you would always want to include it to have the correct warp (it would need to be concatenated internally with the nonlinear warp).
  • If you calculated a warp differently, and you don’t have a linear affine part to concatenate—that is, the WARP dataset is the full and complete warp, then perhaps you could fake an affine transformation that would be reasonable. Namely, make a file, say identity.aff12.1D, containing an “identity” affine transform:

1 0 0 0 0 1 0 0 0 0 1 0

… and provide that as an argument where the affine should go.

How does that work?

–pt

3

perfect!! thank you!