This methodological article proposes a framework for analysing the relationship between cognitive processes and brain activity using variables measured by neurofeedback (NF) carried out by functional Magnetic Resonance Imagery (fMRI NF). Cognitive processes and brain activity variables can be analysed as either the dependant variable or the independent variable. Firstly, we propose two traditional approaches, defined in the article as the “neuropsychological” approach (NP) and the “psychophysiology” approach (PP), to extract dependent and independent variables in NF protocols. Secondly, we suggest that NF can be inspired by the style of inquiry used in neurophenomenology. fMRI NF allows participants to experiment with his or her own cognitive processes and their effects on brain region of interest (ROI) activations simultaneously. Thus, we suggest that fMRI NF could be improved by implementing “the elicitation interview method”, which allows the investigator to gather relevant verbatim from participants’ introspection on subjective experiences.