Dear AFNI experts,
I am processing resting-state data with a script with slight modifications to the one generated by Example 11 from afni_proc.py.
Just for a recap, this pipeline uses, Freesurfer outputs of the T1 and ANATICOR. It doesn’t include band-pass filtering but I have added that myself to the pipeline.
I have a few questions related to this pipeline and I was hoping AFNI experts could help me with those.
One step that I add at the end of the pipeline is that I take certain number of PCA components (say 1, 3 or 5) of the white-matter signal and regress them out of the final residual time-series. My idea is that if the white-matter noise has been taken care of by ANATICOR, then these regressors should not change the time-series, and the resulting connectomes too much. It turns out that the resulting connectomes change, sometime quite a lot. I have attached a scatter plot between connectomes to illustrate this point.
I guess my question is: should this be happening? and also, can we think of ANATICOR and regressing out PCA components of the white-matter signal as complimentary processes, where they can both help with denoising?
When computing enorm from the motion parameters, should we worry about the fact that three of the parameters are linear displacements, while the other three are angular? Should we somehow convert the angular parameters into linear parameters before computing something like enorm or FD?
My EPI dataset has an isotropic resolution of 4x4x4 mm3. What would you recommend as a suitable radius for the localized ANATICOR regressors?
Thanks for this amazing pipeline and I love the QC html that is generated at the end.