There is no really unified doc at the moment, we're just trying to put the different pieces together, and many many pieces are just still missing.
Cartograph is the general name of all the projects we are developing in SHFJ / IFR49 / NeuroSpin or co-developing with partner labs: the final goal is to provide a complete software package for brain cartography. It's a long term goal, of course. So Cartograph includes BrainVISA, Anatomist, and several software projects: AIMS (image processing), VIP (image processing), Sigraph (sulcal graphs processing) and the new Cartograph libraries.
Here are some links to the different projects docs:
.mesh surface format documentation: [PDF] [PS] [LaTeX] [examples]
.tex texture format documentation: [PDF] [PS] [LaTeX]
.bck "bucket" format documentation: [PDF] [PS] [LaTeX]
The sulci nomenclature used by the automatic recognition and morphometry tools
The french document on the JIRFNI training course of may 2006 in Paris
And, of course, here is a link to the web site of BrainVISA and Anatomist:
http://brainvisa.info