Part of the challenge lies in functional brain mapping. Brain functions lie in multiple areas of the brain and appear to be subject to significant individual differences. Addicts will have different reactions to different drug cues, for example. Localized brain functions and mapping are very problematic in some cases. Professor Sinnott-Armstrong explains, "Some mapping is done very well and is very reliable. We know where vision and language areas are. However, mapping is very difficult and controversial for understanding intentions and the control of actions." In neuroscience studies of groups thus far, a functional map can be drawn from an average of the group, yet within that group each person has their own activation pattern, and therefore it becomes difficult to apply group analyses to an individual. While neuroscience mapping needs a baseline for comparison, challenges will arise concerning the makeup of that baseline and if it is the right baseline for a particular individual.

The Project is still deciding how to approach brain mapping and is considering a variety of techniques. One approach might be statistical algorithm pattern classifiers for an individual based upon his or her neuropatterns. Another method may be to look within the group data and see where the variations lie, to get a feel for the different patterns for more reliable inferences. People have different strategies for remembering. If the various patterns can be determined, there is a higher reliability as to what can be inferred about the individual scan. However, such use of brain imaging still has to take into account the particular subject and how he or she remembers. People's memories may be happy or sad, or other preexisting conditions may affect the outcomes of the imaging.

Some legal scholars, practitioners, judges, and scientists also worry that the introduction of brain images into a courtroom or trial setting results in greater prejudice than it adds in terms of probative value. Some believe that when a scientist testifies, he or she will automatically be believed; others feel that in a long trial such testimony will not have as much impact. The actual effect of scientific testimony on jurors is another issue that is being investigated. This is being studied by the MacArthur Law and Neuroscience Project through the use of actual past cases, cutting down the facts to around 500 words - using brain imaging with one group, and no brain image with another. The researchers hope to see if there is a notable difference in verdict. From there, the research will build up to the use of complex cases.

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