This paper presents two significant improvements to the Activation Likelihood Estimation (ALE) method in functional neuroimaging. First, it evaluates two techniques for correcting multiple comparisons: the single threshold test and the False Discovery Rate (FDR) method. The FDR method is found to be more effective in controlling false positives, especially in meta-analyses with small or large numbers of foci. Second, the paper proposes a technique for statistically comparing ALE meta-analyses, which is demonstrated through various tasks such as overt speech in stuttering subjects, the color-word Stroop task, picture-naming tasks, and painful stimulation. The results show that the FDR method provides a more accurate thresholding technique and a reliable method for comparing ALE maps, leading to advanced designs in future meta-analytic research. The study also discusses the impact of the number of foci on ALE results and suggests that the FDR method is the best choice for thresholding ALE maps regardless of the number of foci.This paper presents two significant improvements to the Activation Likelihood Estimation (ALE) method in functional neuroimaging. First, it evaluates two techniques for correcting multiple comparisons: the single threshold test and the False Discovery Rate (FDR) method. The FDR method is found to be more effective in controlling false positives, especially in meta-analyses with small or large numbers of foci. Second, the paper proposes a technique for statistically comparing ALE meta-analyses, which is demonstrated through various tasks such as overt speech in stuttering subjects, the color-word Stroop task, picture-naming tasks, and painful stimulation. The results show that the FDR method provides a more accurate thresholding technique and a reliable method for comparing ALE maps, leading to advanced designs in future meta-analytic research. The study also discusses the impact of the number of foci on ALE results and suggests that the FDR method is the best choice for thresholding ALE maps regardless of the number of foci.