displaced volreg

AFNI Message Board
1

Hi everyone,

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.

2

Hello,

Having the script would be helpful. Could you try to copy and paste the text into a code field in the response box?

-Peter

3

Hello,

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.
https://docs.google.com/document/d/1uP4vYG2rd4V5uOtrIueG8IpsqZtBRyrs49S9fVT-D7Y/edit?usp=sharing
hyperlink to script

4

Hello,

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.

5

Hi Peter,

-giant_move seems to have worked! Thank you so much.