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

------------------ 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0:57 收件人: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu;

主题: 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

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

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

---

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