Hi Alessandra,

I download Cygwin/x through the main site: http://www.cygwin.com.
The direct link is x.cygwin.com.  As I recall (it's been some time),
I used the default download.  Click on the "setup.exe" link to download
a setup file, and then choose "Install from web". The documentation on the site is good.

To compile jip, you need
1) a unix/Linux environment (Cygwin), and
2) X11 libraries.  The required files will be found in /usr/X11R6/lib and /usr/X11R6/include under the cygwin folder.

Hopefully the makefiles that I provide will work without modification.
If you install jip code in "jip-main", then try this:
cd jip-main/build-jip
tcsh
source build-all.tcsh

That will try to build everything, including the required NIFTI, ZLIB, and FFTW components.

Best,
Joe