Dear AFNI experts,

I am in the process of inspecting the QC html output from subject-level preprocessing and analysis of an fMRI dataset using afni_proc.py. I would like to obtain the percentage of censored TRs in each of my task conditions. However, I have noticed what appears to be a strange discrepancy in the values provided in the censor fraction warnings section of the output, which lead me to believe that I either don’t understand the outlier volume censoring process or I have misspecified something in my analysis.

In a nutshell, I have an blocked-design fMRI task with 5 task regressors, which are specified with timing files and regress_basis_multi in afni_proc.py. Rest blocks are not modeled. I am using the default censor motion and censor outlier values from the Example 6b of afni_proc.py documentation. My fMRI scan contains 403 volumes. When I inspect the QC html output (generated by html_review_style pythonic), the General censor fraction warnings tells me the number of censored TRs/volumes out of my total 403 volumes in my scan. However, when I look at the Censor fraction warnings (per stim), the total TRs for each task regressor exceeds the number of TRs that should be associated with each task condition, and the sum of TRs across my 5 task regressors exceeds the 403 volumes in my scan. Additionally, the number of censored TRs per stim exceeds the censored TRs listed in the total General censor fraction warnings output.

I have confirmed that my timing files are accurate, and the X-matrix looks consistent with my timing files. I’m therefore not sure what is happening here. How is afni_proc.py assigning the TRs to different task regressors?

As a side question, I was hoping someone could clarify whether for each TR that exceeds a motion or outlier censor threshold, does afni censor just that TR or the pre/post TR as well?

Many thanks,

Michael