History of AFNI updates  

May 24, 2022 08:24AM
Hi, Osman-

That is a good thing to check. There is even an automatically generated image of seedbased correlation for the DMN in the afni_proc.py generated QC HTML. From your output/results directory, copy+paste:
afni_open -aw QC_*/index.html
... and jump to the "vstat" section. How does that look?

The BOLD effect can be observed outside the brain (meaning here, the final anatomical volume or template brain used for alignment) for various reasons:
+ B0 inhomogeneity geometrically stretches/compresses/distorts the EPI volume, so it doesn't perfectly match the subject anatomical
-> check this in the 'vorig' section of the QC HTML
+ alignment can be imperfect between EPI-anatomical, and/or anatomical-template
-> check this in the 've2a' and 'va2t' sections of the QC HTML, mentioned above
+ the BOLD information measured with FMRI does not measure neuronal activity, but instead blood oxygenation affecting the magnetic field. Blood vessels around the brain can affect the magnetic field greatly (because there some big ones there), so one can see some effects occurring outside the brain at times
+ there can be noise---well, there *is* noise in the data
+ if the EPI data is blurred during processing (as in your case), some signal from inside the brain can get smeared outside a bit

That all being noted, the amount of correlation leaking/overlapping the brain there doesn't seem too terrible to me. But it would be good for you to verify features of your data and processing, noted above.

Subject Author Posted

resting-state fmri analysis Attachments

osman May 21, 2022 09:33AM

Re: resting-state fmri analysis

ptaylor May 24, 2022 08:24AM

Re: resting-state fmri analysis

rick reynolds May 24, 2022 10:08AM

Re: resting-state fmri analysis Attachments

osman June 01, 2022 11:17AM

Re: resting-state fmri analysis

ptaylor June 02, 2022 09:34AM

Sorry, only registered users may post in this forum.

Click here to login