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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
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 CautionDear 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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." DGREVE@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 CautionDear 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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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@nmr.mgh.harvard.edu
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Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Tim Schäfer