Transforming tags with 3dAllineate

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1

Hi,

I have collected a T1w MRI scan using two different scanners for the same patient. In one of these scans, the patient has LPA, RPA, and Nasion fiducials which I have labeled using the “Edit Tagset” Plugin. I want to find the coordinates of these fiducials in the other MRI image where the patient does not have markers on their head. Since I have hundreds of patients like this, I want to find an automated way to do this that is as accurate and efficient as possible.

I tried using 3dAllineate to align the fiducial T1 (containing a tagset) with the other T1, hoping that the tagset would also transform during the process. However, I discovered that the tagset disappeared in the transformed dataset. Is there a way to also transform the tagset? I imagine there must be a way to save out the transformation matrix and then apply it to the coordinates of the tagset, but I’m not sure the easiest way to do this. I know that I could manually edit the tagset in the transformed MRI, but this approach would likely require more time.

Let me know if you have any suggestions!

Thanks

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If you are using only an affine transformation, then you can use Vecwarp to transform lists of coordinates.

https://afni.nimh.nih.gov/afni/community/board/read.php?1,158095,158098#msg-158098
https://afni.nimh.nih.gov/afni/community/board/read.php?1,146048,146181#msg-146181

You can load these tags in from a new file with those new coordinates, or put spheres down instead of “tags” on the new locations.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/rois_corr_vis/suma_spheres.html

If you need to use a transformation that uses both an affine and nonlinear transformations, then you can use the new nl_coords_transform.py. I’ll be adding an affine only option, just for convenience there.