External Email - Use Caution I have to add a last question: 3- how can I generate the -head.fif file from the surfaces I have created (brain_surface, inner_skull_surface corrected with 1mm, outer_skull_surface corrected with -2mm, outer_skin_surface)? I should then use them in MNE
Greatly appreciated! > Il giorno 5 ago 2023, alle ore 17:33, Michelangelo Fabbrizzi > <michef...@gmail.com> ha scritto: > > 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? 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