Hello, I apologize for what is probably a simple issue:
I’ve run the demo single subject analysis with FT data. I would like to be able to use the Whereami atlas tool to see coordinates of areas with activation. Since that only seems to work for data that has been warped to a template, I tried…
Warping the original anat file to the TT_N27+tlrc template with @auto_tlrc function. However, I realized when I tried to overlay the statistic map (stats.FT) that it was, of course, not aligned to the warped anat file.
Running the afni_proc.py script, substituting the newly warped anatomical for the original file. Unfortunately, when I tried to view the results (i.e., overlaying the .stats file on the warped anatomical), they looked wrong (all significant voxels were off the brain, and didn’t at all resemble what it looked like when I viewed the stats.FT over the anatomical before doing any warping).
Do I have to also warp all the original EPI files (with 3dwarp?) before running afni_proc.py, in order to get results to show up correctly? Any guidance would be much appreciated.
To be sure, exactly which script did you run? Was it
If @auto_tlrc overwrote the results, it suggests those
results are already in standard space and you do not
have to do anything.
Thanks for your response.
To clarify, I modified the s01.ap.simple script, so that the input anat file was the one I had warped with @auto_tlrc.
If I understand you correctly, then what I did in my 2nd attempt was correct? What concerned me is that the results in viewer looked quite different from what I saw when I just ran the original s01.ap.simple script on the unmodified data, before trying any warping. However, I reran things and now the two visuals look the same (albeit, I can only view the warped .stats version overlaid onto EPI data; I reference this in Q1 below). The earlier issue may be because I was trying to force AFNI to overlay the .stats file on the FT_anat one…
Two follow up questions:
(1) Why doesn’t AFNI let me overlay the .stats file produced by the warped anat file onto the FT_anat one? (When I try to select the .stats Overlay, it
automatically changes the Underlay to FT_epi_r1 --but it did allow me to overlay .stats on FT_anat originally, before warping the anat.)
(2) Why can’t I use Whereami on the .stats file produced by running running s01.ap.simple? (It works on the warped FT_anat file.)
Bottom line, I just want to be able to look at the results of the analysis and use Whereamai to see where that is! :-S Thanks again!