Hello FreeSurfer exports, I have two questions regarding recon-all flags:
1) Our data was obtained with a 3T scanner. Would you recommend that all 3T data be run thorough the recon-all stream with the -3T flag? 2) One subject has part of the left occipital lobe cut during the skullstripping process. I know how to correct for this (using the -wsthresh flag), but what concerns are there, if any, regarding group analyses combining subjects who were run with adjusted watershed thresholds vs those who were not? Could this bias our analyses? Should all subjects be run through the -recon-all stream with the same watershed thresholds if they will be analyzed together? I appreciate your help and I look forward to your insight. Thanks! Doug Doug Merkitch Neurological Sciences Rush University Medical Center
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