Useful tools for fMRI researchers

Video created with Mango. ROIs created with FreeSurfer and SPMs MarsBar

From the moment we collect the data with the MRI scanner, we need several tools to work with the data. Many researchers have their favourite programming tool to begin converting .dicom files to most commonly .nii (nifti) files. SPM, FSL, AFNI and FreeSurfer are some of the most known and developed toolboxes that are compatible with several operating systems (e.g. OS, Win) and languages (e.g. MATLAB, Python). Beyond those analyses toolbox a researcher also need tools to visualize the data. For this purpose I will share here my favourite softwares to view (f)MRI data.

# 1. Mango

I discovered this tool too late in my opinion (i.e. after completing my PhD). It is a great tool as it is easy to use and visualize your functional data either on template or provided structural MRI data. Besides seeing the results, you can export the results as video or even create a web page to show and share your, for example, T-maps with your colleagues. At the moment this is my favourite tool for data visualization.

# 2. xjview

Another tool that I missed for many years. This tool also allows you to explore your results, with option to threshold with specific p values. Also, you can threshold your t-maps with application of multiple comparisons correction. Highly recommended tool which requires SPM.

# 3. MRIcroGL

This is a lesser known version of a well known tool called MRIcro(n). It is very good to know, slow to use with an old-ish laptop.