Hello,

I am using the HCP pipeline’s task fMRI scripts to process task fMRI data in CIFTI format.

My task is loosely structured as such:

                BOLD 1: contains EV1, EV2, EV3

                BOLD 2: contains EV1, EV3, EV4

                BOLD 3: contains: EV2, EV5, EV6

 

As you can see, not every EV is present in every run. My initial approach when creating the fsf files was to model existing EVs in a given run using the 3 column file input format, and model EVs that don’t exist in a particular run (e.g. EV6 in BOLD 1) as a null EV using the “Empty (all zeros) option. Using this setup, I am unable to create copes nor conduct ftests. I get an error during level 2 of the task fMRI processing script saying some of the contrasts are not linearly independent (or are a linear sum of other contrasts).

Can you please advise whether all EVs (1 to 6 in the above case) need to be modeled in the design matrix/fsf to enable subsequent second level analyses across runs then subjects etc? If so, what is the appropriate way to model an EV that is not present in a given run?

 

Thank you.,

Binyam

 

Binyam Nardos, PhD
Oregon Health and Science University
Postdoctoral Researcher, Fair Neuroimaging Lab

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