Hi Nicola,
I had the problem you described before, and it was because a few subjects had FA values of 0 within the brain. The erode function within tbss_1_preproc would then create a 3x3x3 box of zero voxels centered around the original 0 voxel. These "holes" were then propegated to the mean FA.
My solution was to turn off the eroding by removing the -ero flag from the fslmaths call within the tbss_1_preproc script. The downside to this was the erode function helps to get rid of some of the brighter voxels at the edge of the FA images. To correct for this, I eroded the brain mask and then applied the eroded mask to the FA image. This might not be the perfect solution, but it seemed to work ok.
- Tyler
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