Hello Mans,
Could you provide a bit more detail about the problems you are getting with converting time domain data to frequency domain data in LabVIEW.
There are many different analysis and transform vi's within LabVIEW which you could use. Depending on what your trying to do, you may need to install the Math Interface Toolkit which allows you to communicate to MATLAB from LabVIEW. I don't know if you currently have this installed but if you don't, please find the link to the page on our website below.
http://sine.ni.com/apps/we/nioc.vp?cid=12922〈=US
Hope this helps, please get back to me with more details of your problem and I will be happy to help.
Best regards,
Peter H
Applications Engineer
National Instruments UK