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Dear developers,
We encountered the bug related to the analysis with FLAIR in recon-all (recon-all -s ${subj} -i T1.nii.gz -FLAIR FLAIR.nii.gz -FLAIRpial -all). We obtain a worse segmentation with FLAIR than only with T1. We use FreeSurfer v. 7.3.2 We also tried to run the analysis placing the line PlaceMMPialSurf --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 in the global-expert-options.txt file in the $SUBJECTS_DIR and run recon-all -s ${subj} -FLAIRpial -autorecon3, the output seems better but the pial is ever worst than with only T1. What does the values of mm_min_inside mm_max_inside mm_min_outside mm_max_outside mean? Some suggestions to solve this problem?
Thank you Silvia