> Hi Ravikiran,
>

I don't have any familiarity with the nrrd format beyond looking
here,
but it seems to me that the best mask tools that I know about work best with
nifti files. So I would perhaps convert your data to nifti and then explore
the many tools out there?

Once we have nifti... there are many ways to create masks! A mask is
basically an image that consists of just 0s and 1s (binary), and so if you
multiplied your mask by any sort of image, the resulting image would only
have the original values where you had the 1s, and the spots with 0 will of
course have a value of zero. I know it's silly to explain it, but I
remember a few years back when I figured this out, and thought it was a
pretty neat thing :O)

If you are doing DTI analysis and have an image with FA values, the same
rules apply with regard to the masking - you don't need any sort of special
FA mask, just one of the right orientation / dimensions. Here are some
ideas to get you started:

SPM (run within matlab)
can have the wfu Pickatlas toolbox
which lets you very easily create and save custom masks, and it's all GUI
driven. You can even run Pickatlas standalone from matlab. I would
recommend this if you've never done it before. It's also notable that any
time you do an analysis with a (non binary) image as a mask, it will create
a masked version of the image with the equivalent dimensions.

FSL: contains an FSLUTIL called
fslmathsthat would
let you easily convert any image into a mask. You can also use
their fslview to save a mask.

MRIcron lets you do some
ROI drawing as well, although this is more slice based / manual, and I've
never actually done it.

You can also use more raw methods, like finding an atlas of your choice,
finding the label(s) of the areas you want, and then thresholding and adding
/ subtracting images to get what you like. Matlab has some
scriptsfor
manipulating nifti images, and if you like python I would recommend
nibabel .

Another idea is to use one of the tools above to create the mask, and then
convert it to nrrd and use whatever software you are using for your files.

Best of luck!

-Vanessa