Dear AFNI experts,


I am using BrainSight neuronavigation to precisely target where the fMRI activity is maximal (so-called fMRI-guided TMS).
I realized that I should use the anatomic image in original space, which is in the same space of the original coordinate in raw DICOM files.
I wonder how I can preprocessed T-value map in the preprocessed MNI space (Tvals+tlrc) to the original coordinate of the raw files
to overlay the T-value map.

I searched for previous answers and found 3dWarp and 3dAllineate would work like followings:

cat_matvec subj1_anat+tlrc::WARP_DATA > tlrc_xform.1D
3dWarp -matvec_out2in tlrc_xform.1D -prefix group_warped+tlrc \
-gridset subj1_epi+orig -cubic group_data+tlrc
3drefit -view orig group_warped+tlrc

I followed the code except for the first line...
I guessed the first line was done in the standard preprocessing procedure provided afni_proc.py.
I got the transform matrix, "warp.anat.Xat.1D" which was generated by "cat_matvec subj1.ssMPRAGE+tlrc::WARP_DATA -I > warp.anat.Xat.1D"
So, I used warp.anat.Xat.1D replacing tlrc_xform.1D in the above example...


I expected the functional image (T-value map) was overlapped with the underlying anatomic image in original space.
However, it was not...

Could you answer this question?
If you can, I like to send my data.



Sincerely,
Sungshin Kim