auto_warp: back to the original space

AFNI Message Board
1

Dear AFNI experts:

I have the following pipeline:

  1. auto_warp.py -base TT_N27+tlrc -input t1_ns+orig -skull_strip_input no
  2. do some operations…
  3. 3dExtrema -volume -mask_file -closure -sep_dist 512

What would be the proper way to transfer the xyz point derived from step 3 back to the original space ?
Thanks in advance !!

Yiyu

2

Review the commands to do this in this class handout (roughly slide 38)

https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/afni11_roi.pdf

3

Thank you, Daniel
If the input to be transferred back to the original space is a xyz coordinate instead of an image.
What should I do ?
Is there an AFNI command to handle this ?
Thanks again for the time and help !!

4

Program 3dNwarpXYZ can transform coordinate triples (x,y,z) given a nonlinear warp. Please read the help carefully to make sure you are using this program correctly, because it is easy to specify the nonlinear warp incorrectly.

5

Thank you, Bob

The way I did is:

  1. run auto_warp.py
  2. save the input “point.1D” as x y z (3 column)
  3. cat_matvec -ONELINE anat.un.aff.Xat.1D > orig2tlrc.aff.1D
  4. 3dNwarpXYZ -nwarp ‘INV(orig2tlrc.aff.1D) INV(anat.un.aff.qw_WARP.nii)’ -iwarp input.1D > XYZwarp.1D

Is this correct ?

6

If I were you, I’d look at the xyz points in the original (warped) space where they were created, then look at the transformed points in the unwarped space, and see if they are in the same anatomical location – using the warped anatomical as the underlay in the first case, and the unwarped anatomical as the underlay in the second case. This procedure will quickly inform you if the transformations were applied correctly.

7

Thank you, Bob
This is much appreciated !!