If you shoot raw nef files with your Nikon camera, you may have camera settings that are not readable by non-Nikon applications. One of the most striking ones is if you choose to set the picture controls to create a black-and-white picture. When you open that nef file in Photoshop or Aperture, for example, the colour will come back.
To see this kind of information in non-Nikon applications, you will have to convert the files in a Nikon application. You can for example batch process all your nef files to jpeg or tiff format using View NX (menu File > Convert Files...) or Capture NX (menu item Batch). Then import the tiff files to the other application.
But don't forget that conversion from nef to both jpeg and tiff will lose some data. Tiff is a lossless format, but the only thing that is lossless is what is visible. In the nef file you can always go back and change the picture controls to some other setting. However, there is no way you can get the colour back in a black-and-white tiff file. In other words, it is always good to keep the nef as backup, in case you need to make some other modifications.
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