Hi Bruce，

   The  ‘mris_anatomical_stats‘’ and  'mri_segstats’ command line just output mean thickness of ROI, but I want to know cortical thickness for each vertex in the ROI. So I think the  key is to find the coordination of each vertex in the ROI,but I dont know how. I found that  the RAS coordinates in the lh.cortex.label do not correspond to the coordinates in the lh.thickness.

Hi Kan

you can give the surface-based label to mris_anatomical_stats and it will
constrain it's calculations to the label (where it makes sense):

mris_anatomical_stats -l <path to your label> ...

you can probably do it with mri_segstats too - Doug will know

cheers
Bruce


On Tue, 5
Mar 2019, 310913949 wrote:

>
>         External Email - Use Caution        
>
> Hi bruce??
>    I still have some questions about extracting cortical features of a ROI. I used the
> mri_label2label to sample the volumetric label to the surface of the subject. But I dont know how to
> do next, as i found that the RAS coordinates do  not correspond to the coordinates in the
> lh.thickness, and why?
>     Besides, I found the  web of how to extract cortical thickness values for a region-of-interest
> (ROI) defined in volume
> space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But it doesn't report
> the coordinates information. How can I get the ROI's coordinates information if i use this method?
>     Thanks for your help!
>     Kan Deng
>  
>
>
> ------------------ Original ------------------
> From:  "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>;
> Date:  Fri, Jan 25, 2019 10:58 PM
> To:  "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
> Subject:  Re: [Freesurfer] How to extract cortical features of a ROI
>
> Hi Kan
>
> if you draw a volumetric label you first need to sample it to the surface
> of that subject (mri_label2label --sample). If all you want are stats from
> the subject there is no need to map it to fsaverage - that is only
> necessary if you want to use a group coordinate system.
>
> cheers
> Bruce
>
>
>
> On Fri, 25 Jan 2019,
> 310913949 wrote:
>
> >
> >  External Email - Use Caution
> >
> >
> > Dear Freesurfer Experts,
> >        I want to extract cortical features of a ROI that I drawn manually on  the rawavg.mgz in
> Freesurfer, but i
> > don't know how to do that. I think maybe first the  lesion mask should be registered to the
>  standard templates
> > fsaverage, but I don't know what the command line is , could  you tell me?  And secondly, I should
> use
> > mri_label2label to map the label to individual subject  and extract the cortical features of the
> ROI, am I right?
> >       I am looking forward to your reply!Thanks.
> >
> >                                                   Best wishes!
> >                                                       Kan Deng
> >
> >
> _______________________________________________
> 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