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I currently supply inhomogeneity-corrected (via N4 biascorrection) 3T T1w scans through recon-all pipeline. The correction has solved many segmentation errors which reduced the time spent on manual editing. I have several questions related to this: 1. I am aware of the "3T" flag that can be supplied to recon-all command. It seems redundant to use this flag for already-bias-corrected 3T scans (testing from my end also confirms this), but do you recommend any other bias-correction steps? 2. What are the minimum and maximum intensity thresholds set for GM and WM during recon-all? In the official control point tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0>, it suggests that WM should be "close" to intensity of 110, but I wanted to know the exact thresholds to perform more accurate manual editing. 3. If these GM and WM intensity parameters can be changed from default, do you recommend doing so? If there is a documentation I can refer to find answers (I've failed to find one so far), please let me know. Thank you for your time as always, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115
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