Hello, I am new to fMRI data analysis and following standard tutorials for data processing. But since the
I have two fmriprep preprocessed fMRI in two separate files: fmri1 and fmri2. fmri1 is for condition 1, fmri2 is for condition 2. Using nilearn, I can compute z-map contrasts where condition 1 is active and condition 2 is active, i.e. “condition 1 is 1, and others are 0”, and “condition 2 is 1, and others are 0”
If I want to compute contrasts where “condition 1 is 1, condition 2 is -1, and others are 0”, does it make sense to subtract the z-map where condition 2 is active from the z-map where condition 1 is active?
You typically do not want this, where you two condition of interests come from different runs, since there may be differences in scanner signal between acquisitions due to low-frequency drift and scanner heat. Usually, all conditions you want to compare against each other are in a run (in some block-related or event-related design).
Due to the limitations stated before, if you do want to make a comparison like this, you would want to do everything in a single model while controlling for scanner differences (and not due this subtraction post-hoc as you propose). So, one option is to concatenate your timeseries and design matrices, and include a column in the design matrices for acqusition_1 and acquisition_2, that contain 1s in rows that belong to their respective acquisitions, and 0 otherwise.