There are countless tools for processing MR datasets. Below you'll find the most important ones. Please do not hesitate to contact in case an utmost important is missing and should be listed.
Chris Rorden's most usefull and freely available tool MRIcron is not only a .nii viewer allow for multiple overlay but also for VOI creation. It comes along with DICOM converter dcm2nii and it's GUI dcm2niigui. The package is available for Win, Linux and OSX.
More information and download at: http://people.cas.sc.edu/rorden/mricron/install.htmlMRIcroGL allows you to view 2D slices and renderings of your brain imaging data. It can display many image formats and includes a graphical interface for dcm2nii to convert DICOM images to NIfTI format. It allows you to draw regions of interest which can aid lesion mapping and fMRI analysis. It provides sophisticated rendering.
Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. The Java based package is freely available. FiJI is able to communicate with Matlab. A caveate: processing of NiFTI's comes along with some restriction of Header information. More information and download: https://fiji.sc/
Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about structural and functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release (SPM12) is designed for the analysis of fMRI, PET, SPECT, EEG and MEG. Althrough a standalone version is available Matlab is recommended for sufficient usage. More information and download https://www.fil.ion.ucl.ac.uk/spm/
