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May 10, 2021 12:07PM
Hello there!

I recently used afni_proc.py to pre-process my rs-fMRI data. When I visualised the volreg output and overlaid it onto the final anatomical image, I noticed that there is a bit of misalignment, namely the EPI image seems to be "pulled up" (see image).

I tried with various align cost functions, the -epi2anat option, skull-stripped and un-stripped images but it always seems to end up in this situation.

Since the two images are almost perfectly aligned in the raw data, I was wondering whether there is a way to somehow omit the align step (even though I'm aware that the transformation matrix from it is required for the registration at volreg)?

Any help would be greatly appreciated!

Greetings from (a rather unnaturally sunny) London!

Misho


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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