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Hello FreeSurfer Developers,

I'm attempting to run recon-all -i $workdir/$t1folder/${subj}.nii.gz -subjid ${subj} -all -gcut -clean-bm -3T -mprage -T2 $workdir/$t2folder/${subj}.nii.gz -T2pial -all I have added some pictures to highlight my issue. The issue that I am experiencing it that the T1 (red) adheres to what remains of the skull, while the T1+T2 (blue) underestimates the surface of the cortex. Are thee any solutions to this? And if not, would you recommend to use the T1 alone pr the T1+T2 when proceeding further? In advance I'd like to inform that I have tried to run the multistrip with watershed threshholds ranging from 0.1 to 30, but the gcut just worked better for us rather than trying different watershed threshold levels.

best, Jonas Østerhaug Andersen