Authors of articles published by JMIR Publications do not need our permission to use part or all of an article in their thesis or book. JMIR Publications' articles are published under a Creative Commons Attribution license (see copyright statement on each article), meaning that authors retain copyright (What is a "Creative Commons License"?). Authors can publish their article in a thesis, or as a book chapter, or anywhere else, as long as they adhere to the requirements of the Creative Commons Attribution license, which is basically to cite the original source and to state that it was published (and can be reproduced) under the terms of Creative Commons Attribution license 2.0 (or 4.0 as of June 2017).
Authors should however be aware that -- while they retain copyright and may be able to use their work as book chapter, etc, as long as they disclose that it has been published as journal article in a JMIR journal --, duplicate publication in other journals may be considered scientific misconduct.