Dwi2fod with FA as mask

[jdtournier]

@zeydabadi

I’m using single shell data (+ b0) in the msmt_csd scheme so I’m only getting the wmfod, csf, and GM and as a consequence the wmfod is overestimated (includes the GM tissue?).

Not sure exactly what you mean here, but what we’d recommend with single shell data is to use dwi2fod msmt_csd to produce a 2 tissue decomposition using the WM and CSF responses only, ignoring the GM (see e.g. this post). There’s only 2 b-values, you can’t really estimate more than 2 components with multi-tissue CSD. It does mean that the GM component will end up contaminating both the WM and CSF components to some extent, but it’s still cleaner than single-shell CSD.

@zeydabadi

So, I was hoping by providing a FA map I could somehow help the algorithm to not include some of the GM.

The processing is performed independently per voxel. All the mask does is specify which voxels get processed. So you’ll get the same results as just setting those voxels to zero after the dwi2fod call – it’s certainly not going to affect the results in those voxels that are being processed.

@zeydabadi

BTW, how can I create a binary mask of my FA map in way that FA values between 0.1 and 0.9 maps to 1 and the rest to 0?

Lots of ways:

mrthreshold fa.mif -abs 0.1 mask1.mif
mrthreshold fa.mif -abs 0.9 -invert mask2.mif
mrcalc mask1.mif mask2.mif -mult mask.mif

Or using mrcalc:

mrcalc fa.mif 0.1 -gt mask1.mif
mrcalc fa.mif 0.9 -lt mask2.mif
mrcalc mask1.mif mask2.mif -mult mask.mif

Or better, a one-liner using mrcalc:

mrcalc fa.mif 0.1 -gt fa.mif 0.9 -lt -mult mask.mif