Yes. Please disclose this in the Acknowledgments section of the article, and in your cover letter to the article.
Also, make sure that the article submitted to a JMIR Publications is concise and follows the format requirements for the article type you are submitting. This may mean adapting your thesis length and headings.
Please review Where are your instructions for authors? for details about how your submission must be formatted. Each journal may have slightly different requirements. For example: for the Journal of Medical Internet Research, please visit https://jmir.org/author-information/instructions-for-authors