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May 10, 2021 12:53PM
Hi, Misho-

Sorry to hear that you are having to spend so much time with alignment, rather than being out in the (fleeting) London sun...

It might be useful to see your afni_proc.py command, for starters--could you please copy+paste that here?

The default cost function for EPI-anatomical alignment is lpc (or lpc+ZZ, a modified version for when things are potentially wonky). This usually works well, assuming that the EPI and anatomical start out with good overlap and that the EPI has appropriate tissue contrast. To focus on alignment, one wants to check that sulcal and gyral features line up well, that ventricles overlap well, etc. Namely, that interior and boundary brain regions line up well.

In the image above, the tissue contrast does look a bit low. Can you post the images from the afni_proc.py-generated QC HTML? Namely, the ones from the "vorig" block and the "ve2a" block? That will help diagnose by displaying the raw EPI volume used for alignment, as well as the EPI underlaying the edges of the aligned anatomical.

thanks,
pt



Edited 1 time(s). Last edit at 05/10/2021 01:17PM by ptaylor.
Subject Author Posted

(Mis)alignment Attachments

misho_dimitrov May 10, 2021 12:07PM

Re: (Mis)alignment

ptaylor May 10, 2021 12:53PM

Re: (Mis)alignment Attachments

misho_dimitrov May 11, 2021 08:17AM

Re: (Mis)alignment Attachments

ptaylor May 11, 2021 02:19PM

Re: (Mis)alignment

ptaylor May 11, 2021 02:45PM

Re: (Mis)alignment

misho_dimitrov May 20, 2021 05:33AM

Re: (Mis)alignment

ptaylor June 09, 2021 05:06PM



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