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another question: after the below if I use the command to run autorecon2: recon-all -s sub-01_recon -autorecon2 I get the following error: ERROR: cannot find or read transforms/talairach.m3z Can you help me please? Thanks, regards, Michelangelo > Il giorno 30 lug 2023, alle ore 15:32, Michelangelo Fabbrizzi > <michef...@gmail.com> ha scritto: > > Dear Freesurfer experts, > > I am new to FS, and I would have couple of questions. > I used in sequence: > A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1 > B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon > C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon > > The brainmask.mgz obtained is good (no skull, brain is okay), however if I > now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz > is not used and it is created a new one called ws.mgz that still contain some > piece of skull that generate wrong BEM surfaces; even using -h 5 the result > is not optimal: > mri_watershed -h 5 -useSRAS -surf > /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon > /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz > /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz > > I am wondering: > - how can I force the mri_watershed command to use the brainmask.mgz already > created after step C above, instead of creating a new one? > - is it possible to use the -gcut command also for mri_watershed? > > Thanks, appreciated, > > Miche > >
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