---原始邮件---

发件人: "ts+ml"<ts+ml@rcmd.org>

发送时间: 2018年12月9日(星期日) 凌晨1:15

收件人: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;

主题: Re: [Freesurfer]回复： ?????? 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 <yujunjie828@qq.com> 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
>
>
>
> ------------------ 原始邮件 ------------------
> 发件人: "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>;
> 发送时间: 2018年12月8日(星期六) 凌晨1:16
> 收件人: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
>
> 主题: 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"<fischl@nmr.mgh.harvard.edu>;
> > ????????: 2018??12??8??(??????) ????0:57
> > ??????: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
> > ????: 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
> >
> >
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--
Tim
0176 84273709

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