Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz

2020-04-26 Thread Bruce Fischl
Hi Victor the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.

[Freesurfer] Intensity inhomogeneity messing with the wm.mgz

2020-04-25 Thread Zeng, Victor (BIDMC - Keshavan - Psychiatry)
Hi Freesurfer developers, I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the