External Email - Use Caution
Dear Douglas, dear Bruce,
thanks a lot for your fast and helpful replies, they solved my problem.
For the record: to get the area of my custom surface, I used:
mri_surf2surf --s tim --sval-area graymid --hemi lh --trgval
lh.area.graymid --trg_type curv
If one prefers MGH format over curv, the way to go is:
mri_surf2surf --s tim --sval-area graymid --hemi lh --trgval
lh.area.graymid.mgh
Best,
Tim
> On May 14, 2019 at 4:58 PM "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
> wrote:
>
>
> You can use something like mri_surf2surf --s subject --src-area midsurf
> --hemi --trgval lh.area.midsurf
> run with --help to get examples
>
> On 5/14/2019 10:42 AM, Bruce Fischl wrote:
> Hi Tim
>
> not sure about area (Doug might have something), but for curvature you can do:
>
> mris_curvature -w lh.area.midgray
>
> this will create mean (*.H) and Gaussian (*.K) curvature files. You might add
> a bit of smoothing with e.g. -a 5, which is what we do by default when we
> create the [lr]h.curv files. If we don't have something for area I'll put
> something together for you and you can grab it from dev
>
> cheers
> Bruce
>
>
> On Tue, 14 May 2019, Tim Schäfer wrote:
>
> External Email - Use Caution
>
> Dear list,
>
> I have created a custom surface at 50% thickness between the white and pial
> for my subjects (`mris_expand -thickness lh.white 0.5 lh.graymid`).
>
> Is there a way to compute measures like curv and area for this surface using
> FreeSurfer tools?
>
> An example to clarify: I would like to get a file named lh.area.midgray for
> my new midgray surface, just like I have lh.area and lh.area.pial for the
> white and pial surfaces, respectively.
>
> I have checked the recon-all devtable [1] and it looks like
> `mris_make_surfaces` is used to compute these measures. But it is not clear
> to me whether I could use it for a custom surface as well (and if so, how).
>
>
> Best,
>
>
> Tim
>
> [1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto: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
Best,
Tim
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
