I have a few subjects whose volreg appears to be displaced from their anatomical after running a registration script. I have tried using the xform command and a registration script which incorporates FSL, but neither approach resolved the error.
I am wondering if this is a skull stripping issue, though the subjects’ skull stripped anatomicals do not seem to have any issues.
Please let me know what other info would be helpful. I have not had much success in attaching pictures or scripts to the AFNI message boards in the past but I can try again if those would be useful.
Having the script would be helpful. Could you try to copy and paste the text into a code field in the response box?
Thank you for your response. I have been having issues copying and pasting the script so I’ve tried copying it into google docs and linking it. Please let me know if that works.
hyperlink to script
Thanks for posting the script. Any chance of posting the alignment photos on google as well?
It appears that you used a pretty old version of afni_proc.py to generate the script (2014), so I would first suggest updating your version of AFNI. For the alignment, I suspect that adding “-giant_move” to your align_epi_anat step would fix the issue or in the original afni_proc command that generated the tcsh script to add
-align_opts_aea -cost lpc+ZZ -giant_move
If you suspect a skull stripping issue, then you can use the “new” (circa 2017) @SSwarper[/url] to perform the skull strip and also registration to standard space. Pair that with [url=https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html]Example 6b here and go from there.
If you post the afni_proc commands you write we can help tailor it further. But example 6b should be a good start point for your analysis given the event-related design and options that appear to be used before.
-giant_move seems to have worked! Thank you so much.