Hi! I work on quantification of white matter hyper intensities, but due to demyelinating lesions. To quantify those hyper intensities you can segment it manually on T2w using different available software such as fsl or mipav to create the mask and later quantify them. Otherwise there are some automatic method published for WM lesion segmentation (I think that the problem is quite the same). This is a possible reference: http://www.ncbi.nlm.nih.gov/pubmed/23084503

I hope my answer could be useful.  

What about Magnetiaztion transfer ratio?

White matter hyperintensities can be tricky to analyse because of the different kinds, but we have had some success using FLEX (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905619/). You can get fairly robust total volume estimates from this program, but, as is so often the case, interpretation is the challenge. Hth!

Hi Bryn,

I would recommend using a T2 weighted FLAIR image to quantify the hyperintensity lesions. However, there are many available softwares to do this for you (automatically or semi-automatically) 

MIPAV

JIM

SepINRIA 

Lesion Segmentation Tool (LST) in spm

Most of these softwares require more than one image contrast (T2, T1, and PD)

It turns out that the main contribution to T1 of brain tissue is myelin concentration. The most quantitative paper describing this so far is Stüber C, Morawski M, Schäfer A, Labadie C, Wähnert M, Leuze C, Streicher M, Barapatre N, Reimann K, Geyer S, Spemann D, Turner R. Myelin and iron concentration in the human brain: a quantitative study of MRI contrast. Neuroimage. 2014 Jun;93 Pt 1:95-106. doi: 10.1016/j.neuroimage.2014.02.026. Epub 2014 Mar 6. Since the myelin content is the main biochemical difference between grey and white matter, it makes sense to focus on myelin in trying to understand white matter disorders.

Because so-called T1-weighted images are also proton density and T2*-weighted, and they are not quantitatve, scientifically speaking there is little point in acquiring them. If one really wants to understand white matter pathology, one should use T1 mapping sequences, such as MP2RAGE, and quantitative proton density sequences, such as TAPIR. If fiber structure is of interest, one should use DWI approaches such as DSI, and quantitative susceptibility mapping, which reveals fiber orientations, iron concentrations and diamagnetic inclusions.  'White matter integrity' is a vacuous concept which should be abandoned except in the case of frank white matter disease, such as MS or ALS (see Jones D et al 2013).

I hope this helps.