Dear Keith,
If you reduce the spatial smoothness hyperparameter on the mixels (the -R option) then this
should give you "smoother" transitions. You might also find that the -H parameter has some
influence on this too.
All the best,
Mark
On 21 Sep 2011, at 16:09, Keith Hulsey wrote:
> A few years back I used SIENAX to generate white matter and grey matter probability maps from an MPRAGE to direct my search for white matter hyperintensities in the corresponding FLAIR image. I made a mask of voxels that were mixed between the white matter and the grey matter to use in calculating a threshold for hyperintensity in the white matter.
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> I am responding to a reviewer who noted that using FAST3 in my algorithm is a major limitation since FAST3 is no longer provided with FSL. When I tried to update my algorithm to use FAST4 I got very different results. It seems that the difference is caused by the way FAST4 handles mixels. With FAST3 the transition between white matter and grey matter was more gradual, so using FAST4 I have fewer voxels to calculate my threshold from. Is there a way to control FAST4 so that it handles mixels similarly to FAST3?
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