I am currently stuck on the problem that my resting-state analysis with afni_proc.py results in a flawed outcome. This problem only occurs for my resting-state runs (for all subjects) and not for the task-based runs. The results of the latter are fine.
The problem is that when I open my errts file (e.g. “errts.Subject1_Rest.anaticor+tlrc”) there is activation all around the brain (once I increase the threshold slightly) but not in the brain. Please notice the screenshot that I added, it makes the problem all clear.
Please let me know what you think. Where do you think could the problem be located? In what direction should I look?
By the way: A friend of mine reminded me that I have to use the errts for a resting-state analysis as underlay in the AFNI Gui. I did that. Even if I choose AnatQQ or AnatSS as underlay (and then errts as overlay) the problem remains the same for all kinds of combinations. So I think the problem is not that I simply don’t use the Gui accordingly, but the problem has to be somewhere else.
This is my resting-state analysis script:
for subject in Subject1 Subject2
-blocks despike tshift align tlrc volreg mask blur scale regress
-align_opts_aea -cost nmi
-volreg_tlrc_warp -tlrc_base MNI152_2009_template_SSW.nii.gz
-regress_apply_mot_types demean deriv
-regress_bandpass 0.02 0.2