Dear all,
We are trying to extract a cerebral white matter mask from the Freesurfer output. We are currently using the aparc+aseg file in order to do this, however we realized that the white matter mask (taken by choosing the voxels with values equal to 2 and 41) doesn't correspond exactly to the white matter we would like to have, which rather would follow the WM boundary obtained with the surface processing. Is there a way to get a more accurate mask that corresponds to these boundaries? Also, is there a description of the file format that the surface files are written in?
Thank you,
Antonio
HI Antonio, You can use mris_convert to get the surfaces into ascii format. ie: mris_convert lh.white lh.white.ascii If you look at the file you see the following:
#!ascii version of lh.white 126302 252600 -7.101086 -100.000061 -1.796945 0 -7.231718 -99.740860 -1.915022 0 . . -7.355780 53.003563 -9.506091 0 0 1 2 0 3 2 1 0 . . 120678 121091 121102 0 122524 122217 122525 0
The first line is a comment. The second line lists the number of points and then the number of polygons. The next 126302 lines (number of points) list the x y z co-ordinates of that point. The last 252600 lines (number of polygons) list the points that make up that polygon.
hope that helps, mishkin
On Thu, Feb 21, 2008 at 1:48 PM, Gallo, Antonio (NIH/NINDS) [F] galloa@ninds.nih.gov wrote:
Dear all,
We are trying to extract a cerebral white matter mask from the Freesurfer output. We are currently using the aparc+aseg file in order to do this, however we realized that the white matter mask (taken by choosing the voxels with values equal to 2 and 41) doesn't correspond exactly to the white matter we would like to have, which rather would follow the WM boundary obtained with the surface processing. Is there a way to get a more accurate mask that corresponds to these boundaries? Also, is there a description of the file format that the surface files are written in?
Thank you,
Antonio
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Antonio,
mris_fill will fill the interior of the surface, but this will include things like ventricles, thalamus, etc.... You could take this voxels out using the aseg if you want. The surface formats are documented on the wiki I think, but you might be better off just using mris_convert to change them to ascii, or using the matlab I/O functions we supply.
cheers, Bruce
On Thu, 21 Feb 2008, Gallo, Antonio (NIH/NINDS) [F] wrote:
Dear all,
We are trying to extract a cerebral white matter mask from the Freesurfer output. We are currently using the aparc+aseg file in order to do this, however we realized that the white matter mask (taken by choosing the voxels with values equal to 2 and 41) doesn't correspond exactly to the white matter we would like to have, which rather would follow the WM boundary obtained with the surface processing. Is there a way to get a more accurate mask that corresponds to these boundaries? Also, is there a description of the file format that the surface files are written in?
Thank you,
Antonio
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 -
Gallo, Antonio (NIH/NINDS) [F] -
Mishkin Derakhshan