I found this MNI atlas that some may find helpful. I haven't tried it out yet, though. https://www.martinos.org/resources/aan-atlas

Mai JG, Paxinos G, Voss T (2008) Atlas of the human brain. 3rd ed. Elsevier, Amsterdam. The book comes with a CD that lets you download any or all of the contents, but it's easier to use as a physical, paper book!

For a detailed histological (Nissl) atlas, the best I know is Olszewski J & Baxter D 1982. Cytoarchitecture of the human brain stem, 2nd ed. Basel: Karger. This is not a true 2nd edition, but a reprint of lower quality than the 1st (1954) edition.

Riley HA 1960. An Atlas of the Basal Ganglia, Brain Stem and Spinal Cord. New York: Hafner. This atlas is based on myelin-stained (Weigert) sections. Tracts, including ones not currently believed to exist, are confidently labelled in all the photos.

These three are major works of scholarship, full of detail and with excellent illustrations. Nomenclature (of nuclei, white matter, and unmyelinated fibre tracts) is a headache in the brain stem. The biggest modern "textbook" of human neuroanatomy is Mai & Paxinos (eds) (1912) The Human Nervous System, 3rd ed. Amsterdam: Elsevier-Academic Press. It has I415 big 2-column pages of quite small print, and lots of references. To use a book like this you need to be already familiar with the subject at a level above that of most medical and biological neuroscience courses! As a bridge between the many course-level textbooks and detailed neuroanatomical atlases, I recommend Parent, A. (1996) Carpenter's Human Neuroanatomy, 9th ed. Baltimore: Williams & Wilkins.

I'm an author of Barr's The Human Nervous System (10th ed, 2014), a neuroanatomy textbook for medical students, neurology residents etc. that includes references for further study at the end of each chapter.

John Kiernan, Anatomy, UWO, London, Canada.

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Thank you very much, John. Those are exactly what I'd like to know!!

I found the book Mai JG, Paxinos G,Atlas of the human brain. 2nd ed. Elsevier, Amsterdam in the library of our univeristy. First I'll check it out.

I want to read your neuroanatomy textbook, so I follow you in RG.

Thank you so much.

I like Dr. Naidich's "Duvernoy's Atlas of the Human Brain Stem and Cerebellum" (ISBN: 978-3211739709) Look into this since it may be the best out there with regard to correlation with MRI, however it may not have the level of detail regarding the functional role of some of the structures that you seek. I have found this to be extremely helpful for clinical studies, in particular neoplasms and stroke. I may use some other sources for supplemental information on the function of a given structure, but identification of the structures on MRI is the real strength of this book.

Dr. Naidich's book uses post-mortem high field strength MRI to show exquisite detail. This is not clinically reproducible, however gives guidance on getting additional information on clinical examinations.

Thank you very much, Kay. 　It is very useful information.

I'll go to that website and check the course.Thank you so much.

Thank you very much, Asim.

I am going to use proton-density weighted image to identify some anatomical structures in the brainstem. So I want atlas, especially including the comparison with MRI. I'm very interested in the atlas you told me. I'm planning to use stroke patient, so that atlas will be very useful for me. I want to get the atlas ASAP. Thank you.

Are any of the atlases noted above available in MNI space? Any MNI atlas with ROIs for some of the smaller nuclei (e.g., dorsal motor nucleus, etc.)?

Unfortunately, there is a complete lack of atlases in MNI space. You have to measure the distance between landmarks (e.g. obex, AC, PC) and convert between atlases and MNI. What is worse is that the slice tilt will be wrong in most cases.

Thanks. I feared as much.