[Freesurfer] ???????????? ?????? Calculated thickness
External Email - Use Caution Dear Tim, I have used chmod to give this file permission. I want to know because this instruction is no longer available? yours yujunjie ------ ??: "ts+ml" : 2018??12??9??(??) 1:15 ??: "Freesurfer support list"; ????: Re: [Freesurfer]?? ?? Calculated thickness External Email - Use Caution Just to be sure, could you also post the output of the following command: who am i; ls -ld /usr/local/freesurfer/subjects/groupstudy/ I suspect that you do not have write access to /usr/local/. Unless you are running FreeSurfer as root (which you definitely should not do), you should not be allowed to write into /usr/. I suggest you try changing the output directory to some place where definitely have write access. You could do something like this: mkdir ~/groupstudy/ mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white -out_name ~/groupstudy/lh_std_10.mgh -absmean ~/groupstudy/lh_absmean_10.mgh -mean ~/groupstudy/lh_mean_10.mgh -absstd ~/groupstudy/lh_absstd_10.mgh /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh Best, Tim > On December 8, 2018 at 2:08 PM 1013364183 wrote: > > > External Email - Use Caution > > Dear Bruce, > I run the following command: > > mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white > -out_name $SUBJECTS_DIR/groupstudy/lh_std_10.mgh -absmean > $SUBJECTS_DIR/groupstudy/lh_absmean_10.mgh -mean > $SUBJECTS_DIR/groupstudy/lh_mean_10. Mgh -absstd > $SUBJECTS_DIR/groupstudy/lh_absstd_10.mgh > /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh > > > The results are as follows: > Perform 60 steps of smoothing of input data > Using /usr/local/freesurfer/subjects/groupstudy/lh_std_10.mgh as output file > Using /usr/local/freesurfer/subjects/groupstudy/lh_absmean_10.mgh as output > file for abs-mean > Using /usr/local/freesurfer/subjects/groupstudy/lh_mean_10.mgh as output file > for mean > Using /usr/local/freesurfer/subjects/groupstudy/lh_absstd_10.mgh as output > file for std-of-abs-mean > Reading /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh... > Smooth input data by 60 steps > Stats over surface (318651 vertices): mean = 0.0888528, std = 0.334772, > absmean = 0.23932, absstd = 0.250386 > > > > But I did not get the generated mgh file.Is this what is the reason? > > > > yours yujunjie > > > > -- ???? -- > ??: "Bruce Fischl"; > : 2018??12??8??(??) 1:16 > ??: "Freesurfer support list"; > > : Re: [Freesurfer] ?? Calculated thickness > > > > Hi yujunjie > > in general if you want our help you have to give us more information. We > need for example the full command line you ran and the full output of it > (in text, not a screen shot!) > > cheers > Bruce > On Sat, 8 Dec 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > The problem is in the fourth step of ThicknessRepeatibility - > > mris_surface_stats > > > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??12??8??(??) 0:57 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Calculated thickness > > > > Hi yujunjie > > > > you can use mris_distance_transform -vol to compute a volumetric map of > > distances to the surface if that is what you want. > > > > cheers > > Bruce > > On Fri, 7 Dec 2018, > > 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS?? > > > I now have two different surfaces, the two surfaces have intersecting > > > parts, I want to calculate > > > their signed distance, what should I do?I want to calculate the thick std > > > and mean mgh files > > through > > > mris_surface_stats, but there is no output. What is the reason? > > > > > > yours yujunjie > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Tim 0176 84273709 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? ?????? Calculated thickness
External Email - Use Caution Dear Bruce, I run the following command: mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white -out_name $SUBJECTS_DIR/groupstudy/lh_std_10.mgh -absmean $SUBJECTS_DIR/groupstudy/lh_absmean_10.mgh -mean $SUBJECTS_DIR/groupstudy/lh_mean_10. Mgh -absstd $SUBJECTS_DIR/groupstudy/lh_absstd_10.mgh /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh The results are as follows: Perform 60 steps of smoothing of input data Using /usr/local/freesurfer/subjects/groupstudy/lh_std_10.mgh as output file Using /usr/local/freesurfer/subjects/groupstudy/lh_absmean_10.mgh as output file for abs-mean Using /usr/local/freesurfer/subjects/groupstudy/lh_mean_10.mgh as output file for mean Using /usr/local/freesurfer/subjects/groupstudy/lh_absstd_10.mgh as output file for std-of-abs-mean Reading /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh... Smooth input data by 60 steps Stats over surface (318651 vertices): mean = 0.0888528, std = 0.334772, absmean = 0.23932, absstd = 0.250386 But I did not get the generated mgh file.Is this what is the reason? yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??12??8??(??) 1:16 ??: "Freesurfer support list"; ????: Re: [Freesurfer] ?? Calculated thickness Hi yujunjie in general if you want our help you have to give us more information. We need for example the full command line you ran and the full output of it (in text, not a screen shot!) cheers Bruce On Sat, 8 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > The problem is in the fourth step of ThicknessRepeatibility - > mris_surface_stats > > > -- -- > ??: "Bruce Fischl"; > : 2018??12??8??(??) 0:57 > ??: "Freesurfer support list"; > : Re: [Freesurfer] Calculated thickness > > Hi yujunjie > > you can use mris_distance_transform -vol to compute a volumetric map of > distances to the surface if that is what you want. > > cheers > Bruce > On Fri, 7 Dec 2018, > 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS?? > > I now have two different surfaces, the two surfaces have intersecting > > parts, I want to calculate > > their signed distance, what should I do?I want to calculate the thick std > > and mean mgh files > through > > mris_surface_stats, but there is no output. What is the reason? > > > > yours yujunjie > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ?????? Calculated thickness
Hi yujunjie in general if you want our help you have to give us more information. We need for example the full command line you ran and the full output of it (in text, not a screen shot!) cheers Bruce On Sat, 8 Dec 2018, 1013364183 wrote: External Email - Use Caution The problem is in the fourth step of ThicknessRepeatibility - mris_surface_stats -- -- ??: "Bruce Fischl"; : 2018??12??8??(??) 0:57 ??: "Freesurfer support list"; ????: Re: [Freesurfer] Calculated thickness Hi yujunjie you can use mris_distance_transform -vol to compute a volumetric map of distances to the surface if that is what you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS?? > I now have two different surfaces, the two surfaces have intersecting parts, I want to calculate > their signed distance, what should I do?I want to calculate the thick std and mean mgh files through > mris_surface_stats, but there is no output. What is the reason? > > yours yujunjie > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? Calculated thickness
External Email - Use Caution The problem is in the fourth step of ThicknessRepeatibility - mris_surface_stats -- -- ??: "Bruce Fischl"; : 2018??12??8??(??) 0:57 ??: "Freesurfer support list"; ????: Re: [Freesurfer] Calculated thickness Hi yujunjie you can use mris_distance_transform -vol to compute a volumetric map of distances to the surface if that is what you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS?? > I now have two different surfaces, the two surfaces have intersecting > parts, I want to calculate > their signed distance, what should I do?I want to calculate the thick std and > mean mgh files through > mris_surface_stats, but there is no output. What is the reason? > > yours yujunjie > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? Calculated thickness
External Email - Use Caution Dear Bruce, I want to implement ThicknessRepeatibility, but I can't get the output mgh file in the last step. What is the reason? http://ftp.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility yu'jun'jie -- -- ??: "Bruce Fischl"; : 2018??12??8??(??) 0:57 ??: "Freesurfer support list"; ????: Re: [Freesurfer] Calculated thickness Hi yujunjie you can use mris_distance_transform -vol to compute a volumetric map of distances to the surface if that is what you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS?? > I now have two different surfaces, the two surfaces have intersecting > parts, I want to calculate > their signed distance, what should I do?I want to calculate the thick std and > mean mgh files through > mris_surface_stats, but there is no output. What is the reason? > > yours yujunjie > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Calculated thickness
Hi yujunjie you can use mris_distance_transform -vol to compute a volumetric map of distances to the surface if that is what you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: External Email - Use Caution Dear FS?? I now have two different surfaces, the two surfaces have intersecting parts, I want to calculate their signed distance, what should I do?I want to calculate the thick std and mean mgh files through mris_surface_stats, but there is no output. What is the reason? yours yujunjie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Calculated thickness
External Email - Use Caution Dear FS?? I now have two different surfaces, the two surfaces have intersecting parts, I want to calculate their signed distance, what should I do?I want to calculate the thick std and mean mgh files through mris_surface_stats, but there is no output. What is the reason? yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
