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Summary: The integration of neuroimaging and transcriptomics data, Imaging Transcriptomics, is becoming increasingly popular but standardized workflows for its implementation are still lacking. We describe the Imaging Transcriptomics toolbox, a new package that implements a full imaging transcriptomics pipeline using a user-friendly, command line interface. This toolbox allows the user to identify patterns of gene expression which correlates with a specific neuroimaging phenotype and perform gene set enrichment analyses to inform the biological interpretation of the findings using up-to-date methods.For complete details on the use and execution of this protocol, please refer to Martins et al. (2021).