As described in this tutorial: https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion?highlight=(HLU)#Adjust_the_reference_head_position
I ran with the default settings
But, couldn't find change in head distance as described in the mentioned tutorial. I am not sure - what am I missing out.
Your screenshot shows the process "refine registration", not "adjust coordinate system".
Apologies for the wrong snapshot earlier. I ran the following command
and see the following alignment (before-upper; after-lower)
I observe some part of helmet is within the skull post adjustment.
Also, there is no change in distance variation as opposed to the description in the tutorial:
I then, ran refinement using the following option:
and find the refinement better than post "adj-co-ordinate-system".
I am not sure - what part am I missing in correcting the head displacements. Can you help me here?
Please take care in the options you select. I don't think the images all correspond here. The "after" picture you show would be what I'd expect if you ONLY selected to "reset coordinates". The alignment is very bad since it was based on the automated MNI registration.
In your screenshot you selected both "reset" AND "refine with head points", so your "after" picture should have looked like your final picture since "refine" is the same in this process and the one through the right-click menu.
But the head motion tutorial is mainly about the other option you did NOT select: "adjust head position to median location".
I got this!