Does anyone have experience in performing volumetric reconstructions of MRI? Which software is the most recommended? What literature is available for consultation?
There are dozens of free software packages that can do this. For example, basic reconstruction visualization can be done in seconds using MRIcro/MRIcron/MRIcroGL/Aliza/ImageJ etc, to more comprehensive packages such as FSL and FreeSurfer. Have a look at Part 1 of my ebook:
GIve our Checkpoint software a try. It can load MRI in DICOM format, perform 3D rendering, and extract 3D surfaces. It also has several built-in tools for 3D shape analysis.