Sure, there are hundreds of them. Most libraries that have medieval manuscripts have at least some, if not all, of them digitized. Here's some Avicenna, one of the more important medical tracts in that era.

That's from the British Library, they have many others online (and many that aren't). BSB, BAV, Leiden, Switzerland. For instance here's) a Swiss manuscript of Al-Razi.

wanting to understand the mind of a "medical doctor" of that time

I don't see how the best way of doing that be to read a single treatise or two, compared to a book that's actually about explaining medieval medicine and which already has distilled the insight of surveying many sources and drawn conclusions from them? Written by someone who's spent years and years studying this stuff full-time? In other words, a textbook from some academic. For instance Nancy G. Siraisi's, Medieval and Early Renaissance Medicine- An Introduction to Knowledge and Practice, (University of Chicago Press, 1990).

But I generally prefer straight from the source.

Why? What makes a single source better, and what makes a single manuscript a good source even for one text? Historians don't usually read from digitized manuscripts unless there's a specific reason to. Manuscripts are written with handwriting, sometimes very poorly legible handwriting, and even when not, are filled with abbreviations, non-standard spelling, no paragraph breaks or modern punctuation, as well as errors and editing. These are manuscripts, not printed books. In manuscripts the only texts that only have a single version are texts tend to be ones that only exist in a single copy.

Historians who want an actual text of something tend to consult an edition of the text, preferably a critical edition that draws on multiple (or even all) manuscripts of a particular text and compares them and attempts to reconstruct the original text as best as possible.

In other words, reading a single manuscript of Avicenna won't tell you everything about medical medicine; it won't necessarily even tell you what they thought Avicienna said as that one manuscript might say X where every other manuscript in existence says Y; and you won't know unless you go repeat the research that goes into a critical edition.

Even better though would be to start with some anthology like Wallace's Medieval Medicine: A Reader that gathers translations of the most popular texts from multiple periods.

If you really consider it best to go read the manuscripts directly, by all means do so. If illustrated or with illuminations, they can be very nice to look also nice to look at too. But frankly they're more an annoyance than anything to actually read from, compared to a modern edition.