Hi all,
I'm new to FreeSurfer and I was wondering if there are any methods or software to read the ?h.thickness files and perhaps as a result get a list or table of all the vertices and their corresponding thickness? Also, is there a way to convert the vertex-based thickness files into voxel-based thickness data?
Thanks in advance and best regards, Kevin
Hi Kevin
you can use mris_convert to change the thickness to an ascii file by doing (from the surf directory)
mris_convert -c thickness ./lh.orig ./lh.thickness.asc
you can then sample that back into the volume using mri_surf2vol:
mri_surf2vol --surfval ./lh.thickness --hemi lh --fillribbon --subject \ bruce --o ../mri/lh.thickness.mgz --identity bruce --template \ ../mri/norm.mgz
cheers Bruce
On Wed, 9 May 2012, Kevin Chen wrote:
Hi all,
I'm new to FreeSurfer and I was wondering if there are any methods or software to read the ?h.thickness files and perhaps as a result get a list or table of all the vertices and their corresponding thickness? Also, is there a way to convert the vertex-based thickness files into voxel-based thickness data?
Thanks in advance and best regards, Kevin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Kevin, for the first part you can run mri_convert lh.thickness --ascii+crsf lh.thickness.dat For the 2nd part, you can use mri_vol2surf. Like most of our commands, you can run those with -help or --help to get more docs. doug
On 05/09/2012 12:53 PM, Kevin Chen wrote:
Hi all,
I'm new to FreeSurfer and I was wondering if there are any methods or software to read the ?h.thickness files and perhaps as a result get a list or table of all the vertices and their corresponding thickness? Also, is there a way to convert the vertex-based thickness files into voxel-based thickness data?
Thanks in advance and best regards, Kevin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry, that should be mri_surf2vol
On 05/09/2012 02:26 PM, Douglas N Greve wrote:
Hi Kevin, for the first part you can run mri_convert lh.thickness --ascii+crsf lh.thickness.dat For the 2nd part, you can use mri_vol2surf. Like most of our commands, you can run those with -help or --help to get more docs. doug
On 05/09/2012 12:53 PM, Kevin Chen wrote:
Hi all,
I'm new to FreeSurfer and I was wondering if there are any methods or software to read the ?h.thickness files and perhaps as a result get a list or table of all the vertices and their corresponding thickness? Also, is there a way to convert the vertex-based thickness files into voxel-based thickness data?
Thanks in advance and best regards, Kevin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Kevin Chen