Surface area of subcortical structures

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FW: questions about the surface...

longitudinal study

Elizabeth Selgrade

16 Sep 2009 16 Sep '09

2:51 p.m.

Hello,

Is there a way to get the surface area of FreeSurfer subcortical structures?

Thanks, Liz Selgrade

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Douglas N Greve

16 Sep 16 Sep

3:05 p.m.

There's not an easy way. You could binarize the structure (mri_binarize), then build a surface around it (mri_tessellate), maybe smooth it (mris_smooth), then compute the surface area (mris_info). This would be a completely untested method though:).

Elizabeth Selgrade wrote:

...

Hello,

Is there a way to get the surface area of FreeSurfer subcortical structures?

Thanks, Liz Selgrade _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Nick Schmansky

3:16 p.m.

or use mri_extract_label instead of mri_binarize, like this, to get the left hippocampus:

mri_extract_label aseg.mgz 17 lh.hippo.mgz mri_tessellate lh.hippo.mgz 128 lh.hippo.unsmoothed mris_smooth lh.hippo.unsmoothed lh.hippo mris_info lh.hippo |& grep total_area

this seems to work.

'17' is the index for left hippocampus, as found in $FREESURFER_HOME/FreeSurferColorLUT.txt

Nick

On Wed, 2009-09-16 at 15:05 -0400, Douglas N Greve wrote:

...

There's not an easy way. You could binarize the structure (mri_binarize), then build a surface around it (mri_tessellate), maybe smooth it (mris_smooth), then compute the surface area (mris_info). This would be a completely untested method though:).

Elizabeth Selgrade wrote:

...
Hello,

Is there a way to get the surface area of FreeSurfer subcortical structures?

Thanks, Liz Selgrade _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Bruce Fischl

3:33 p.m.

sure, you could use mri_tessellate to cover it with triangles, then mris_info to get the surface area. You'll need to get the structure index from the FreeSurferColorLUT.txt file to pass to mri_tessellate

cheers, Bruce

On Wed, 16 Sep 2009, Elizabeth Selgrade wrote:

...

Hello,

Is there a way to get the surface area of FreeSurfer subcortical structures?

Thanks, Liz Selgrade _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Bruce Fischl
Douglas N Greve
Elizabeth Selgrade
Nick Schmansky