convert warp file from AFNI FSL

AFNI Message Board
1

AFNI version info (afni -ver): Version AFNI_22.0.09 'Hadrian'
Hello,

I have a2b.1D and a2b+orig. files generated from align_epi_anat.py.
How can I convert these files to be recognized by FSL's commands?

Thank you very much.
Ashley

2

Copying a BRIK/HEAD file is as easy as:

3copy a2b+orig a2b.nii.gz

for example.

The affine transformation format is pretty different between the two software. I don't know of a simple way to do that.

--pt

3

Thanks for your suggestion .
I have tried this.
When I used FSL command (applywarp) to apply it, the error was reported:
'An error occured while reading file: a2b.nii'

4

Hi, Ashley-

Could you please copy+paste your align_epi_anat.py command?

I don't think align_epi_anat.py outputs a warp dataset---that would only output when the estimated warp is nonlinear (and hence a whole dataset is needed to describe local shifts/warps), which would be estimated by 3dQwarp, @SSwarper, @animal_warper, etc. The main output in terms of alignment parameters is the set of affine parameters: (by default) 12 numbers that represent shifts, rotations, shears and scalings of a dataset. Affine parameters are global, hence apply to stretch or rotate the whole dataset, and so only the 12 numbers are needed in either "matrix" or "parameter" form---hence it would be good to know what command you actually ran, for getting this registration information out.

The dataset output by align_epi_anat.py is most likely the one showing the source dataset aligned/registered to the base one, hence I guess it is a 3D volume only to be overlayed on the reference/base one. (Note: a nonlinear warp dataset would typically have three subvolumes, each representing a local shift along a different dimension.)

--pt