Diffusion tensor estimation from a manually segmented brain mask

Support
1

Hey There,

I tried to do get an “output DTI volume” with a manually segmented brain mask, but it didn’t work.

My workflow (using Version 5.6.2):

Generated a automatic brain mask > convert lablemap to segmentation node > used the DWI volume as the source > edited the the brain mask via segmentation > exported lablemap as binary lablemap > diffusion tensor estimation to create a new output DTI volume … what I see now is a frozen slice of the manual brain mask

When I create a DTI Volume with the automatically brain mask it is all working.

I would be super thankful for help :folded_hands:t3:

2

Not sure what you mean by this one.

In any case, I suggest you estimate the tensors from the DWI, then calculate the FA from the tensors and then apply the mask to the FA scalar volume.

Also 5.6.2 is pretty old. SlicerDMRI may not have changed much since then but we generally suggest always using a recent supported version (you can have more than one version on your machine at the same time).