Dear Mouna,

Sorry for the late answer. I never managed to have NIAK run on Windows. Unfortunately, so far the simplest option you have is to install a virtual machine to run Ubuntu from windows. I'd recommend the fantastic neurodebian (http://neuro.debian.repository that comes with a large number of preconfigured packages (including minc). Not all the tools necessary to use NIAK come with neurodebian, but there is enough to read/write minc. You can compile the whole minc bundle easily on ubuntu (instructions here http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall). I have started a small project that may work for you if you only need to read minc. It is using the native HDF5 libraries of Matlab, and does not require any additional software (i.e. it will work without an install of the Minc tools).
http://code.google.com/p/mominc/

This is an on-going (half finished) project, and you will need to pull out the code directly from the subversion repository. But in most cases the reader works fine. In the long term it will be more robust than the current MINC reader/writer implemented in NIAK.

I hope this helps. Best regards,

Pierre