Hi everyone
I have found some problems in the skull stripping step of my MRI images analysis. The skull was successfully removed but not the whole membrane. I tried to solve that mistake reducing the threshold in the mri watershed algorithm (from 25 to 5) but the problem remain (image 1). The amount of not removed membrane in the volume is high and therefore the manual erasing is very tedious. When I applied the step 2 of the program to segment the brain structures FreeSurfer misclassified some pixels of the membrane as cerebral cortex (image 2). I'm afraid that the cortical thickness can be computed in a wrong way in the nearest areas of the misclassified pixels. Is there any automatic procedure to resolve that problem?
Thanks in advance
Abel
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