(Original post by TheSownRose)
JPEG files are ok, but the problem with them is every change you make degrades the quality ... so I'm thinking you processed them and, in doing so, lost some of the colour information.
NEF files are what Nikon call their raw files. A raw file (you may also see people call it a RAW, capitalise it; it's not a format in itself, it doesn't need capitalisation) is basically a digital negative. What happens when you take a photo in JPEG format is the camera takes a raw photo, but then does some of its own processing, discards some of the information and gives you a JPEG. For a lot of people, JPEGs are fine, they often end up decent enough. But if you're going to be doing some processing to it, especially arty things like this, you ideally want to work with the raw files. The raw files keep all of the information, so you are choosing what to use and what to get rid of in the processing. They also don't degrade as you change them, they retain their quality.
The first issue to address: you don't know how to work with raw. That's fine, it's not inate knowledge, anyone that does use them learnt how to. I like to use Adobe Lightroom to process my raws; it is quite expensive, but bear in mind either a) you're a student so it'll be a lot cheaper for you and b) if you only need it for a short while, you can download a trial version from Adobe
for 30 days. As for learning how to use it: Scott Kelby, The Adobe Photoshop Lightroom 3 Book for Digital Photographers
- it is for Lightroom 3 and the trial available is Lightroom 4; from what I've read and seen, the changes are mostly in the organising system, not the processing system which you are interested in. Kelby's book is fantastic, but make sure you're sitting at the computer and going through it rather than reading away from the computer. It's mainly chapter 4 you'd want - Editing Essentials.
You may be wondering why you should use raw instead of JPEG, so I quickly knocked up this example for you. It is of a flower; I have chosen this photo because I took it to trial a lens and I will never use it for anything else.
This is the JPEG my camera decided to produce:
This is the black and white conversion from that JPEG:
This is the colour processing I did on the raw file:
This is the black and white conversion I did after colour processing the raw file:
This is when I converted the raw to black and white and then
I always shoot in colour and then convert to black and white if I want to have it as black and white. I also convert and then process, not process it as a colour and then convert.