> Hi Gulay,
NIFTI (.nii) file formats are the most common way of reading, processing and analyzing MRI image files. If you would like to use MATLAB to analyze your data, then you can download spm12 and follow the tutorials for preprocessing and analyzing data. You can use the NIFTI tools toolbox available on the MATLAB file exchange if you just want to load the .nii files and apply your own methods for preprocessing.

Here are some resources to help you get started:

https://www.mathworks.com/matlabcentral/...

http://andysbrainblog.blogspot.com/2012/...

http://www.fil.ion.ucl.ac.uk/spm/

I hope this helps,
Shady El Damaty