Hi, I've been consistently getting errors in surface reconstruction in the subgenual area of the cingulate - the grey matter gets missed completely, and instead, both the pial and white surfaces run along the grey/white boundary (see attached). The aseg seems to be ok, labelling the region as cerebral cortex (also see attached). I've tried control points and various other fixes but can't seem to adjust it. Any suggestions re: what to do? this happens consistently on just about all my images (they are Phillips 3T). Thanks, Alex
Hi Alex,
sorry, this is an unintended consequence of the code that prevents the surface from deforming into non-cortical structures. I'll see if I can fix it and get you a new version.
cheers, Bruce On Thu, 19 Apr 2007, Alexander Fornito wrote:
Hi, I've been consistently getting errors in surface reconstruction in the subgenual area of the cingulate - the grey matter gets missed completely, and instead, both the pial and white surfaces run along the grey/white boundary (see attached). The aseg seems to be ok, labelling the region as cerebral cortex (also see attached). I've tried control points and various other fixes but can't seem to adjust it. Any suggestions re: what to do? this happens consistently on just about all my images (they are Phillips 3T). Thanks, Alex
That would be great. Thanks Bruce.
Hi Alex,
sorry, this is an unintended consequence of the code that prevents the surface from deforming into non-cortical structures. I'll see if I can fix it and get you a new version.
cheers, Bruce On Thu, 19 Apr 2007, Alexander Fornito wrote:
Hi, I've been consistently getting errors in surface reconstruction in the subgenual area of the cingulate - the grey matter gets missed completely, and instead, both the pial and white surfaces run along the grey/white boundary (see attached). The aseg seems to be ok, labelling the region as cerebral cortex (also see attached). I've tried control points and various other fixes but can't seem to adjust it. Any suggestions re: what to do? this happens consistently on just about all my images (they are Phillips 3T). Thanks, Alex
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is this something the rest of us need to worry about? I've been checking some of my data and don't believe I'm finding the same problem as Alex. Thanks.
-Derin
Hi Alex,
sorry, this is an unintended consequence of the code that prevents the surface from deforming into non-cortical structures. I'll see if I can fix it and get you a new version.
cheers, Bruce On Thu, 19 Apr 2007, Alexander Fornito wrote:
Hi, I've been consistently getting errors in surface reconstruction in the subgenual area of the cingulate - the grey matter gets missed completely, and instead, both the pial and white surfaces run along the grey/white boundary (see attached). The aseg seems to be ok, labelling the region as cerebral cortex (also see attached). I've tried control points and various other fixes but can't seem to adjust it. Any suggestions re: what to do? this happens consistently on just about all my images (they are Phillips 3T). Thanks, Alex
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think it depends on what version you are running. If the midline surfaces don't move, then it might be. Hopefully the newest version fixes these problems.
cheers, Bruce
On Mon, 23 Apr 2007, Derin Cobia wrote:
Is this something the rest of us need to worry about? I've been checking some of my data and don't believe I'm finding the same problem as Alex. Thanks.
-Derin
Hi Alex,
sorry, this is an unintended consequence of the code that prevents the surface from deforming into non-cortical structures. I'll see if I can fix it and get you a new version.
cheers, Bruce On Thu, 19 Apr 2007, Alexander Fornito wrote:
Hi, I've been consistently getting errors in surface reconstruction in the subgenual area of the cingulate - the grey matter gets missed completely, and instead, both the pial and white surfaces run along the grey/white boundary (see attached). The aseg seems to be ok, labelling the region as cerebral cortex (also see attached). I've tried control points and various other fixes but can't seem to adjust it. Any suggestions re: what to do? this happens consistently on just about all my images (they are Phillips 3T). Thanks, Alex
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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Alexander Fornito -
Bruce Fischl -
Derin Cobia