hello Gulay!

.nii is the standard extension of NIFTI images. NIFTI is a format used in neuroimaging for all kinds of structural and funcitonal images recostructed from the dicom images during acquisition (https://nifti.nimh.nih.gov/nifti-1). As far as I know you cannot directly read them in matlab (while you can read Analyze images), however you can by means of some matlab scripts provided by other softwares. What I do is to use the script provided by FSL (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a popular suite of software for analyzing and visualizing neuroimaging data. If you work on a mac or *nix, the installation is pretty straightforward. After that, in the fsl/etc/matlab/ folder you will find read_avw and save_avw, to read and write NIFTI images into and from matlab, respectively. 

In any case, before installing this, you can visualize your NIFTI images in one of the many free visualizers available. I particularly like Mango (http://ric.uthscsa.edu/mango/download.ht...). In this visualizer, you can also load all the 3D volumes of an fMRI image at once, and navigate through them by enabling Edit -> Series Labels from the menu of the window where the image will be displayed.

Have fun with neuroimaging! :O)

all the best,
leonardo