If you don't currently have a cooler installed it wouldn't be a bad idea to pull out a small ruler(or carefully use a measure tape, being careful not to scrape or damage anything) and measure how much clearance you have to work with from center of CPU slot, knowing how much space is available makes things much easier when choosing a suitable cooler as nigh on every supplier provides measurement specs for their coolers.
That PCI-E slot does look pretty close compartively with a regular ATX(or other Mini-ITX) board and i'd be worred about many coolers with a 120mm+ width fitting(just because of how the CPU is situated on that particular board), here's a 92mm noctua(NH-U9S) on that board which is still pretty close but also confirmed to fit in
this review. I'm sure it'll depend on particular cooler, but i'd not expect any given 120mm cooler to fit just as a result of the very limited space and you would possibly have to change orientation(which may affect cooling).
Have managed to dig up a small amount of different builds using that board thanks to google, here's a pic using the Silverstone SST-NT06-PRO(quite snug but bigger fan and priced around the same as the Noctua).
EDIT: This is actually a slightly different MSI board, the non-gaming AC model but images show clearance around the socket is practically identical.
Here's an example of the CoolerMaster TPC812 being installed on that board, note the orientation change(same would likely apply to using any other 120mm cooler).
Here's another low profile cooler on the board - the Cryorig C1, this is pretty much out of the question if your ram is taller than the HyperX ram in the image and is priced another good £10+ over both the Noctua and Silverstone.
If any of the images don't work(pulled from digging around on google so may be hotlink protected), lemme know and i'll provide direct links to the pages they're on.