The personal choices are many. Graduate school is arguably the best opportunity to learn research principals, technical skills and an experimental system. From this standpoint, it is advantageous to choose a research area that you are considering to continue within your career, at least in general terms. In this regard, it is essential that you ask yourself if the environment you choose will make you a better research scientist.
Motivation to do the project is also essential. The reasons for this motivation may vary but a level of passion for the project is often a major part of obtaining success. You have to be in a lab environment in which you are comfortable. Does the style of the supervision match the way in which you work best? Can you interact productively with other members of the group? Other considerations such as lab location, stipend, course load and other program requirements might seem more trivial but need to be considered.
Your success is closely linked with that of the principal investigator (PI) who will supervise your project. It is therefore very important to consider his/her characteristics. As mentioned above, the supervisory style of the PI must match your working style.
Is he/she available for consultation? Will you have suitable independence in deciding the direction of the research? These answers can often best be obtained by speaking with other members of the lab.
You need to also address whether other graduate students have been successful under the PI"s supervision. Where and what have current students and recent graduates published? Have recent graduates been successful in obtaining fellowship awards? One must also consider the funding status of the PI. Has he/she demonstrated success in obtaining research funds? Is the project in which you are most interested satisfactorily funded? What becomes quickly apparent is that there are many questions to ask when choosing a research project.
As a student, you can and should feel free to seek advice from members of the MD/PhD Committee, the Departmental Graduate Chair, students, co-workers and the PI.