Hello,
Is there a way to get the surface area of FreeSurfer subcortical structures?
Thanks, Liz Selgrade
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
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
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
freesurfer@nmr.mgh.harvard.edu