Hi Angela,

You can use the `fslstats` command line tool to extract FA or MD over a specific mask.
So a command like
fslstats <FA_image> -k <thalamus_mask> -M
will give you the mean FA over the thalamus mask.
Just type `fslstats` in the command line to see an overview of all the output options.

Cheers,

Michiel

> On 12 Mar 2018, at 15:15, Angela Bernabeu Sanz <[log in to unmask]> wrote:
>
> Dear experts,
> I am performing an analysis to understand the effect of thalami atrophy in some cognitive tests.
> I got my FA and MD maps, and the segmented thalami masks from each subject. I would like to extract the global FA and MD values from the segmented thalami but I have not come across to ant manual or detailed script about how to perform it.
> Can anyone help me? Thanks in advance.
> Angela