External Email - Use Caution Dear Lilla,
Thanks for your reply. Could you kindly point me to the skullstripping tool for pediatric data? Does it need InfantFS or works also with FS standard version? Appreciated, Mic > Il giorno 11 gen 2024, alle ore 18:02, Zollei, Lilla,Ph.D. > <lzol...@mgh.harvard.edu> ha scritto: > > HI Mic, > For pediatric data (not sure what age range you are processing), we use a > different skullstripping tool. That might be useful for you. Let me know if > this is stil of interest to you. > Best, Lilla > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Michelangelo > Fabbrizzi <michef...@gmail.com <mailto:michef...@gmail.com>> > Sent: Saturday, August 5, 2023 11:33 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping > > External Email - Use Caution > Dear Experts, > > I reran -autorecon1 with the -expert option adding in the file xopts.txt: > mri_normalize -mprage -b 20 -n 5 -gentle \n mri_watershed -h 5 -atlas > -useSRAS -surf sub-01_recon > > This improved a lot the surfaces, however the inner_skull and outer_skull > surfaces, are still crossing (I suspect this is due to the fact that I am > using pediatric data and the shift of the surfaces are too big maybe?). > So I created a new inner_skull and outer_skull surfaces giving a shift of > +1mm and -2mm respectively using Freesurfer commands: > mris_expand sub-01_recon_brain_surface 1 sub-01_recon_inner_skull_surface > mris_expand sub-01_recon_outer_skin_surface -2 > sub-01_recon_outer_skull_surface > They are now much better, see attached screenshots (before shift correction > and after it). > <Surfaces_without_shift_correction.png> > > <Surfaces_with_shift_correction.png> > > I would have two questions for you: > 1- it looks the brainmask.mgz still contain three pieces of skull (see > screenshot below)…is there any other way to remove them (-less removes too > much)? better if from command line, otherwise even manual intervention > 2- is it possible to force mri_watershed to use a smaller value of the shift > when it generates the inner_skull and outer_skull surfaces from the > brain_surfaces and outer_skin_surface (instead of using another command after > it as I did with mris_expand)? > > I greatly appreciate your help and thank you in advance for it! > > Miche > > > <Schermata 2023-08-05 alle 17.20.04.png> > > > >> Il giorno 1 ago 2023, alle ore 00:22, Douglas N. Greve >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> ha scritto: >> >> External Email - Use Caution >> >> there are not options to autorecon1 specifically. You can pass some >> watershed args on the command line, but it is probably easier to use an >> expert options file, eg, create a text file (eg, xopts.txt) with something >> like >> mri_watershed -less >> then run recon-all with -expert xopts.txt (and the rest of your args) >> You can add as many options as you want to that line >> >> On 7/31/2023 1:22 PM, Michelangelo Fabbrizzi wrote: >>> 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> <mailto: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 >>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>> <freesurfer-boun...@nmr.mgh.harvard.edu> >>>> <mailto: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 >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>; fsbuild <fsbu...@contbay.com> >>>> <mailto:fsbu...@contbay.com>; freesurfer-ow...@nmr.mgh.harvard.edu >>>> <mailto: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 <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be >>>> https://secure-web.cisco.com/1_wHF3HF_pCokVMVjI9dTiFhpRIePceldnU_dJWAo1kjm6tx9G4dni994-CXxlfMQkl1D4ECVO9xtLEPvY84aGsau_ZcEmqfE5mYXZ0pga3vd9hPbMIg2IgIEv8S5UC2wBqN6AKiy9xN_3rCxqJReFBPDZH84-VfaZDu3sJr6NiyNfmWoArCPFpBiIvATGH-liBEh2ukvy45mYuKmq_NcGIhHLI5W7I0i55Nt7V1TlqczSQ5pfHs5eiBEf9MVOQscCgj4cKc-BKviYOfNoaTWVrGv6qiPFIwzZZ88H-XcCLHLwphmp43Q9C3EwB1urTUTG6hxhUlrAPNfBqxWD3AmEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> <https://secure-web.cisco.com/15k8N-Zo4AKDYaXF49SR8hi6D1Ts33kcqH2-zVmVVMdx_wYSEpXxC-rSwtJiecx6qlFIVgt-51BJOM5LZsE_ljTF9wwpyXuoQ3wI-wmss1Z7NEk1k9V7Y2gOts_89x281g-1Fh0WLdVN7mXlzRSFr20A7N0R2BmRGbNX-tB5mQlz7HTEKagZoiun9I6gbpgn_Flj9imjx5uDE_3yqNiUikyZaiG9bE5hdaPAoYN87fqNiuiYAo7gEtm8XR2vvArrr/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. 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