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The query is technical in nature. Let me first try to clarify the use of the word "baseline" in medicine . "Baseline" basically refers to a line on a sports field, such as the one in tennis, that marks the end of the playing area, or the one in baseball that marks the path along which players run. The meaning of baseline in medicine is very similar to that of the running baseline (baseball) being the direct path that a base-runner is taking to the base he is in route to. This word has been incorporated in the field of medicine. Here, the word "baseline" refers to an imaginary line used as a starting point for making comparisons. In the give sentence the comparison is done between the baseline evaluation and the evaluation done again after six months. The baseline evaluation pertaining to FBC (Full blood count) and LFT (Liver function test)measures current or pre-treatment parameters (e.g., chemistries, cell counts, enzyme levels, etc.), against which response(s) to therapy, if any, is (are) evaluated. A baseline in medicine is information found at the beginning of a study or other initial known value which is used for comparison with later data.

Now that the term "baseline" as used in medicine has been explained, let me dwell on the grammatical function of the preposition "at" in the given sentence. The meaning of "baseline" as explained in the paragraph above is "starting point". we say "at the starting point of the study". "At" is the appropriate preposition when one is talking about the starting time when an event takes place.