Re: [Freesurfer] mri_watershed and improvements of skullstripping
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. > 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> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Michelangelo > Fabbrizzi mailto:michef...@gmail.com>> > Sent: Saturday, August 5, 2023 11:33 AM > To: Freesurfer support list <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). > > > > > 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 > > > > > > >> Il giorno 1 ago 2023, alle ore 00:22, Douglas N. Greve >> 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 >>> >>> Your help is greatly appreciated! >>> >>> Michelangelo >>> >>>> Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing >>>> <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> >>>> >>>> <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 >>>> <mailto:fsbu...@contbay.com>; freesurfer-ow...@nmr.mgh.
Re: [Freesurfer] Infant fs
External Email - Use Caution Dear Lilla, I posted a similar question some week ago, I quote it here again, I would be grateful if you could provide feedback. Regards, Mic From: Michelangelo Fabbrizzi mailto:michef...@gmail.com>> Date: Wednesday, October 11, 2023 at 11:48 AM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Sennott, Liam Ricker mailto:lsenn...@mgh.harvard.edu>> Subject: Use of infantFS and FS in the interval 2 - 4.5 years of age External Email - Use Caution Dear FS experts, I see it is recommended to use infantFS below 2 years of age, whereas FS has been used for 4.5 years and above. I was wondering what could be used in the interval 2 - 4.5 years of age: which are benefits and drawbacks of both? Thanks, appreciated, Mic > Il giorno 9 gen 2024, alle ore 09:45, Zollei, Lilla,Ph.D. > ha scritto: > > Hi Amrita, > > The download link has been sent to you. > > The thalamus does get segmented with infantFS and the LUT is the same as for > the adult recon. I would process the 11 year old data with the adult pipeline. > > Lilla > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Amrita Pal > mailto:palamritaor...@gmail.com>> > Sent: Monday, January 8, 2024 7:17 PM > To: fsbuild mailto:fsbu...@contbay.com>> > Cc: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Infant fs > > External Email - Use Caution > Thanks. I had filled out the form. How long do they take to respond? Also can > I do subcortical thalamic segmentation with it? How is the LUT calculated > both for infants and adults? Would you recommend an eleven year old's data > analyzed by regular FS or infant FS? > > On Mon, Jan 8, 2024, 6:19 PM fsbuild <mailto:fsbu...@contbay.com>> wrote: > > Looks like you need to fill out the request form, > > MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" > claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/infantFS > <https://secure-web.cisco.com/1dbtViRCP-0PLBypuF1Fj5qzAlPhc6KTriifPd6VDcWqF7xoGy5_RmCV9DESmq-vaRo-3N5IHH2TF6rrMRpO_rF9o-kVYjt32iOlxPl8QdsktF5angxtW8maDgywS6T2YemC-feHV4fj6xzNwsF-bcF4f6D-486xYs5tvXzZ3QQQqprCWXEfQWZ10W7sJI4Q9iu-cCqW3oX3tcfBBRIxhtN4BZpqC7wE6rtr_5SyH2ky7iZnp1ETsueZg0hPI5Ezeyu9Sc9HeqRXpJA3m3GHf1yVhw3opouW0WgOjcBZjX3kf13zML6zkRAuSlXTBO1YHihUgFjfkymA-I1e8pwsYtg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FinfantFS> > > - R. > >> On Jan 8, 2024, at 18:12, Amrita Pal > <mailto:palamritaor...@gmail.com>> wrote: >> >> External Email - Use Caution >> >> Hello >> >> I am trying to use the infant fs for processing my pediatric data. Where can >> I download the package? >> >> Thanks and Regards >> Amrita >> ___ >> 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 >> behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://secure-web.cisco.com/1q3i3hm3EROnrywxosdE0h5G5Lm9CLsKtE888a1uJOI697jTlhSteRGHD1e9f0Pc5BgfMduNYdiePtUTRKglQB4qo28DStCrpMs8Ewe4ZuuBxkx2OqLIq_SsQbLxPHWjT5eflEk-7aNOfWOE0oU0-Gx237c_QgiAl0jgieZgVTWJoLSU94UHK-6PwGPEcEV2fTGiWUvBZ8ANkSN7kxRjXdZGgWerFallwZqBtrFCcDIY6qxMRSj8QSGTKSxsT0W1xdH0knHXFojd8P4ln5LGoqESukGtlDXID5GR2Q9BDjMFV8cj7bx2J5RS3fcKc48la92IOiw-5nLG3PPKMOk2gpA/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> > https://secure-web.cisco.com/15HrOQdxTWLpZpmOwvGl6vMGOQHIjwEsR0WcnsiObzRYrg_EB3l9SujTDV3FExqLhOy1KTN3asft-ATWBUBWUiBIXqz79cP1nQWC0BJoThKFOdRNbgyFScDcRgyi7ppGCq5sDck3_sCbj5wo5c2Gkrt1FQJQVcC7kYudGVwzJs3MRLs8YA1VK3dmOw_9wZKdhiMjriAIlDnmjWdHGLr_MFXMbC0DkFPyCe05KRBf3_rq4Jq3kF_hijuBf8tOMosAXvpL6-Jt54Hl82UwlEz6IYN76tylq9PIhlyMmrc3_cfhzrn3v0JmLCKLwDr-ibiyp/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
[Freesurfer] Use of infantFS and FS in the interval 2 - 4.5 years of age
External Email - Use Caution Dear FS experts, I see it is recommended to use infantFS below 2 years of age, whereas FS has been used for 4.5 years and above. I was wondering what could be used in the interval 2 - 4.5 years of age: which are benefits and drawbacks of both? Thanks, appreciated, Mic ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] Use of infantFS and FS in the interval 2 - 4.5 years of age
External Email - Use Caution Dear All, any feedback? Appreciated! Regards, Mic > Il giorno 2 ott 2023, alle ore 17:27, michefabb ha > scritto: > > > Dear FS experts, > > I see it is recommended to use infantFS below 2 years of age, whereas FS has > been used for 4.5 years and above. > I was wondering what could be used in the interval 2 - 4.5 years of age: > which are benefits and drawbacks of both? > > Thanks, appreciated, > > Mic ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] mri_watershed and improvements of skullstripping
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 > 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). > > > > > 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 > > > > > > >> Il giorno 1 ago 2023, alle ore 00:22, Douglas N. Greve >> 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 >>> >>> Your help is greatly appreciated! >>> >>> Michelangelo >>> >>>> Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing >>>> <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> >>>> >>>> <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 >>>> <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 -sku
Re: [Freesurfer] mri_watershed and improvements of skullstripping
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 Your help is greatly appreciated! Michelangelo > Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing > 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 > On Behalf Of Michelangelo Fabbrizzi > Sent: Sunday, July 30, 2023 9:32 AM > To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; > 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> > . ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use CautionDear Yujing,yes, I am using FS 7.3.2, so thanks I will try withrecon-all -s sub-01_recon -autorecon2 -caregshould I add the -careg also for the -autorecon3 step?Can you eventually have a look also at the questions in my first email below (at the very bottom of this email trail)?Greatly appreciated!Il giorno 31 lug 2023, alle ore 14:51, Huang, Yujing ha scritto: External Email - Use Caution Hi Michelangelo, I’m wondering if you are using FS 7.3.2? ‘DOCAREG’ was accidentally dropped for autonrecon2. You can fix it by adding ‘-careg’ at the end of command line. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Michelangelo Fabbrizzi Sent: Sunday, July 30, 2023 11:34 AM To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; freesurfer-ow...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping External Email - Use Caution Dear All, 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 ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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://www.massgeneralbrigham.org/complianceline .___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use Caution Dear All, 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 > 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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] Problem installing FreeSurfer
External Email - Use Caution Dear all, thanks for your reply. I did as below and the first time I run the command “freeview”, it works. Then if I try to open it again, it gives the same error as below…can you help me please? Thanks, appreciated, Michelangelo > Il giorno 31 mag 2023, alle ore 23:43, fsbuild ha > scritto: > > > Please make sure you have downloaded a freesurfer license.txt file by filling > out the form at, > https://secure-web.cisco.com/1hc5Xc7px__3EjuoO1_Ni4orsJzMv2R3iM-TJ3g17W6pD1Jv2-zP7lu8luJ73VfXWqrsbHX_7eZc4dqW0qWuk88NFuUNQxZ7E35P7PaGZrx3_HXCb5RW8jZWDDtzYCB_ukWSy3Fz5lbERnNvMc0l8SgVPh66EIA3pkAdAz9x6wHNX_sxP2xYQ4KCLPgHYRndbQ5stn4tNAVOQ7iNJMa_86RhGR2kP6sEXQ_MQzPRxYuQdUq-PQnSOzmYT1KnKZFMtzRCEAgwtXdhwDvUybAWLzyl6qjmND8kf0yQveUBT1m0eM_PHPXIOqS9cs64lCoxG/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html > > <https://secure-web.cisco.com/1hc5Xc7px__3EjuoO1_Ni4orsJzMv2R3iM-TJ3g17W6pD1Jv2-zP7lu8luJ73VfXWqrsbHX_7eZc4dqW0qWuk88NFuUNQxZ7E35P7PaGZrx3_HXCb5RW8jZWDDtzYCB_ukWSy3Fz5lbERnNvMc0l8SgVPh66EIA3pkAdAz9x6wHNX_sxP2xYQ4KCLPgHYRndbQ5stn4tNAVOQ7iNJMa_86RhGR2kP6sEXQ_MQzPRxYuQdUq-PQnSOzmYT1KnKZFMtzRCEAgwtXdhwDvUybAWLzyl6qjmND8kf0yQveUBT1m0eM_PHPXIOqS9cs64lCoxG/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html> > > Place the license.txt file you will receive in your home directory, e.g., > > $ cd $HOME > $ head -1 license.txt > > > Set the FS_LICENSE environment variable manually (and/or in your shell > initialization file, e.g., .bashrc) to point to the license file, > … here set from a terminal window running bash shell ... > > $ export FS_LICENSE=$HOME/license.txt > > Setup the freesurfer environment, > > $ export FREESURFER_HOME=/Applications/freesurfer/7.4.0 > $ source $FREESURFER_HOME/SetUpFreeSurfer.sh > freesurfer-darwin-macOS-7.4.0-20230504-55dcf98 > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer/7.4.0 > FSFAST_HOME /Applications/freesurfer/7.4.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/7.4.0/subjects > MNI_DIR /Applications/freesurfer/7.4.0/mni > > $ which freeview > /Applications/freesurfer/7.4.0/bin/freeview > > Then try running freeview with no arguments to see if it brings up an empty > window, > > $ freeview > > If that works, quit freeview and try running it again with an example volume > included in the distribution, > > $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz > > If that works, quit freeview and try your own surface/volume files. > > - R. > >> On May 31, 2023, at 17:05, Michelangelo Fabbrizzi >> wrote: >> >> External Email - Use Caution >> >> >> Dear Sirs, >> >> I am new to Freesurfer. I installed as shown on website and added the >> license.txt, however when I open freeview I get an error >> "/Applications/freesurfer/7.4.0/bin/freeview: riga 2: 2047 Segmentation >> fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“” >> Attached the report. >> >> Freesurfer version: freesurfer-darwin-macOS-7.4.0-20230510-e558e6e >> Platform: MacOS12.6.6 >> Mac: Macbook Pro Intel Core i5 dual-core >> XQuartz2.8.15 >> XQuartz2.8.5 >> Can you help me please? >> >> Thanks! >> >> Michelangelo >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Problem installing FreeSurfer
External Email - Use CautionDear Sirs,I am new to Freesurfer. I installed as shown on website and added the license.txt, however when I open freeview I get an error "/Applications/freesurfer/7.4.0/bin/freeview: riga 2: 2047 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“”Attached the report.- Translated Report (Full Report Below) - Process: freeview [2074] Path: /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview Identifier:org.martinos.freeview Version: 7.3.2 (100) Code Type: X86-64 (Native) Parent Process:bash [2073] Responsible: Terminal [1299] User ID: 501 Date/Time: 2023-05-31 23:02:37.7243 +0200 OS Version:macOS 12.6.6 (21G646) Report Version:12 Anonymous UUID:0FF1F8BB-D74E-EBFE-3D6D-3F90E594D1DE Time Awake Since Boot: 2500 seconds System Integrity Protection: enabled Crashed Thread:0 Dispatch queue: com.apple.main-thread Exception Type:EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x02280021 Exception Codes: 0x0001, 0x02280021 Exception Note:EXC_CORPSE_NOTIFY Termination Reason:Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [2074] VM Region Info: 0x2280021 is not in any region. Bytes after previous region: 2366109110306 Bytes before following region: 103182294319071 REGION TYPESTART - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL mapped file 118c4-118e83000[ 2316K] r--/rwx SM=COW ...t_id=d4d67611 ---> GAP OF 0x5ffee717d000 BYTES MALLOC_NANO 6000-6800 [128.0M] rw-/rwx SM=PRV Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 freeview 0x102019b98 0x101e26000 + 2046872 1 QtWidgets 0x1136ef413 QWidget::event(QEvent*) + 1283 2 QtWidgets 0x11382e5a4 QMainWindow::event(QEvent*) + 276 3 QtWidgets 0x11369f0b7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 4 QtWidgets 0x11369fffc QApplication::notify(QObject*, QEvent*) + 508 5 QtCore 0x1147d71da QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 6 QtWidgets 0x113706de4 0x113693000 + 474596 7 QtWidgets 0x113704d5a 0x113693000 + 466266 8 QtWidgets 0x11369f0b7 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 9 QtWidgets 0x11369fffc QApplication::notify(QObject*, QEvent*) + 508 10 QtCore 0x1147d71da QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 11 QtGui 0x112b6e82d QGuiApplicationPrivate::processGeometryChangeEvent(QWindowSystemInterfacePrivate::GeometryChangeEvent*) + 493 12 QtGui 0x112b6f036 QGuiApplicationPrivate::processWindowScreenChangedEvent(QWindowSystemInterfacePrivate::WindowScreenChangedEvent*) + 470 13 QtGui 0x112bc729c 0x112ae6000 + 922268 14 libqcocoa.dylib0x113cdba50 0x113c92000 + 301648 15 libqcocoa.dylib0x113cd48c9 0x113c92000 + 272585 16 libqcocoa.dylib0x113cd437c 0x113c92000 + 271228 17 QtGui 0x112bb893e QWindowPrivate::create(bool, unsigned long long) + 206 18 QtWidgets 0x1136ddd9d QWidgetPrivate::create() + 1037 19 QtWidgets 0x1136db881 QWidget::create(unsigned long long, bool, bool) + 321 20 QtWidgets 0x1136dd8e7 QWidgetPrivate::createWinId() + 103 21 QtWidgets 0x1136dd8e7 QWidgetPrivate::createWinId() + 103 22 QtWidgets 0x1136dd8e7 QWidgetPrivate::createWinId() + 103 23 QtWidgets 0x1136dd8e7 QWidgetPrivate::createWinId() + 103 24 QtWidgets 0x1136dd8e7 QWidgetPrivate::createWinId() + 103 25 QtWidgets 0x1136dd8e7 QWidgetPrivate::createWinId() + 103 26 QtWidgets 0x1136de631 QWidget::winId() const + 65 27 freeview 0x102121964 0x101e26000 + 3127652 28 freeview 0x10212188f 0x101e26000 + 3127439 29 freeview 0x101eb159f 0x101e26000 +
