description of auto_warp.py output files

AFNI Message Board
1

Hi all,

I've run auto_warp.py with the following command
auto_warp.py -base MNI152_2009_template.nii.gz -input T1.nii.gz -suffix _al_MNI -overwrite

I've got the following output files in ./awpy, but I am not sure what some of the 1D files are:

anat.nii # T1 image in original space
anat.un.nii # T1 image in original space after 3dUnifize
base.nii # MNI template
anat.un.aff.nii # T1 image in MNI space after affine transformation?
anat.un.aff.qw.nii # Warped T1 image in MNI after nonlinear warping, i.e. final output anat.un.aff.qw_WARP.nii # Warping coefficients (3 volume brick)

anat.un.aff.Xat.1D
anat.un.aff.nii.Xaff12.1D
anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft.1D
anat.un.aff.maskwarp.Xat.1D
anat.un.aff.nii_WarpDrive.log

My issue is that I want to compute the inverse transformation from MNI to T1 space with 3dNWarpCat, but I don't manage to get it right. Could you please help me?

Thank you very much
Cesar

2

Salve, Cesar!

How about:

# create the one-line version of this initial shift:
cat _matvec -ONELINE anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft.1D \
    > anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft_ONE.1D

# the warp, concatenating everything to go from src->base, 
# and then inverting it
3dNwarpApply                                                                 \
    -overwrite                                                               \
    -master     anat.nii                                                     \
    -source     MNI152_2009_template.nii.gz                                  \
    -nwarp      "anat.un.aff.qw_WARP.nii anat.un.aff.maskwarp.Xat.1D anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft_ONE.1D" \
    -iwarp                                                                   \
    -prefix     TEST3

I leave the prefix filename in there, because it was not obvious how to do this.

--pt

3

Oh, and if you want the 3dNwarpCat command to create the full inverse warp:

# concatenation to make new warp, but see comment below
3dNwarpCat \
     -warp1 "anat.un.aff.qw_WARP.nii" \
     -warp2 "anat.un.aff.maskwarp.Xat.1D" \
     -warp3 "anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft_ONE.1D" \
     -iwarp \
     -prefix FULL_WARP_INV.nii.gz

# and then apply
3dNwarpApply \
     -master anat.nii \
    -source MNI152_2009_template.nii.gz \
    -prefix TEST4 \
    -nwarp FULL_WARP_INV.nii.gz

Comment: doing this initially led to my warped result being cropped a little bit. I think I would directly do the 3dNwarpApply command, from the prior post. But if you want to go this route, you might need to add -expad .. to the 3dNwarpCat command, to expand the warp size.

--pt

4

thank you so much Paul

5

Great, glad that worked.

We should definitely have this in the auto_warp.py help, will add it there soon. Thanks for asking about this.

--pt