External Email - Use Caution Dear Yujing,
thanks again for your help, just a last question, how can give to autorecon1 the input to use certain options at the mri_watershed step (for instance a certain preflood height (-h 5) or use of the atlas option (-atlas))? recon-all -s sub-01_recon -i T1w.nii.gz -autorecon1 xxxx Your help is greatly appreciated! Michelangelo > Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing > <yhuan...@mgh.harvard.edu> ha scritto: > External Email - Use Caution > > I'm not sure how to force mri_watershed command to use the brainmask.mgz > already created. > > Recon-all '-gcut' is achieved by running mri_gcut after mri_watershed. > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Michelangelo Fabbrizzi > Sent: Sunday, July 30, 2023 9:32 AM > To: freesurfer@nmr.mgh.harvard.edu; fsbuild <fsbu...@contbay.com>; > freesurfer-ow...@nmr.mgh.harvard.edu > Subject: [Freesurfer] mri_watershed and improvements of skullstripping > > External Email - Use Caution > > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1cF5CFj8ObeEdVU_l8xNGBdbJJ0PpzQ0VrSp5AzRUYXgIxGRUfeyVxaZ9CYyltHFOjkFZr3L3v8Sj-Q43KuOROdbHN-BlQ3kEJGstPNrP89sh3tzlULMEJfhOIV7yDG5cLd7US9Kdx53lxH37tG4cbcrN_SIdEfVaeujvuwgCe_pY9kNgRR711jNjJ2Gju8uAvp6b5417gKL24XKNTz3S6v3aZhiUihlhwcdxG299RmBHNNN8FcuFLe-cD6e0ldB-GgQiuKLGfy6Wc1IOUQpuKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1cTHii2jK1prD_CnADwRM4fGIQbTqO7yHAtvDOSHvIUNYRGRbxoZMXfSSnHb33WRj4ejM84mowaRwVZIGGyJqCffQc13gzZrBbUUGiNSxMnsPaonRdhTOwLQ3GhEnjxTWH6EHJ3dEtgWtzTJ8TfcgSZVu9ka4oSJ5fleh_m5gi0LveysoML4KLApySqFDDOfdGx4JaHXemN9lCXDCMje-jp-_qskKNhXbY-yP-V_CvrOlx4E5V60bcJv7j063TumpulbZYMv0vxWR9Vcmg6w2GsNDCNMmQO1llRCYoTGhj3koFztD4iKLZRJQU4aG0qLQbPaSJWYdnZW-u7Wp9V2k9w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General Brigham > Compliance HelpLine at > https://secure-web.cisco.com/19ZF3Eo2hejHW73PfG4iB-XcRcs7fDWd8GwCtm3h9M_CC3_u6UtvHsVzHGJ-1ZaDUpHru1S1350N_ophruGMIVTSUAv64GW-Hwy_XyWmghNedfA49x6wRn00_gB0ImsWecfgk-dZV6zDjqYm-SO-bvmNVa-Ef1VWLS5LsKI0Jg_XBgMJ5b732gLMmCbhfEKJSepG9O0C8raL9wICrMzY89GNBrSv7dTYxKxxdLKCUIzdyircSGYJ8bI-SXqUeemRvcRtOTWchnl6BVYrtEQhzg_HfULERNoDWNcgo6IVkMQt-6628n4GLwL1ikksBbpWBzc_8Slb_7LKNXneCZrN6oA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <https://secure-web.cisco.com/19ZF3Eo2hejHW73PfG4iB-XcRcs7fDWd8GwCtm3h9M_CC3_u6UtvHsVzHGJ-1ZaDUpHru1S1350N_ophruGMIVTSUAv64GW-Hwy_XyWmghNedfA49x6wRn00_gB0ImsWecfgk-dZV6zDjqYm-SO-bvmNVa-Ef1VWLS5LsKI0Jg_XBgMJ5b732gLMmCbhfEKJSepG9O0C8raL9wICrMzY89GNBrSv7dTYxKxxdLKCUIzdyircSGYJ8bI-SXqUeemRvcRtOTWchnl6BVYrtEQhzg_HfULERNoDWNcgo6IVkMQt-6628n4GLwL1ikksBbpWBzc_8Slb_7LKNXneCZrN6oA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > .
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