Hi Antonella,
the surfaces look fine. As for the cerebellum, I don't think the watershed did that - it's too even. What does the orig.mgz look like?
cheers Bruce On Thu, 14 Jul 2011, Antonella Kis wrote:
Good morning Bruce,
Looking back to the Slice No.82 I am attaching now the brainmask for this slide. While switching between brainmask and wm.mgz my opinion is that I shouldn't add any vertex on the wm.mgz on the right hemisphere. Is this correct? I am not sure about the bottom part. It looks like part of the cerebellum had been removed. Should I adjust the watershed threshold by passing the -wsthresh flag to recon-all?
Thank you very much for your help. Antonella
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 13, 2011 4:51 PM Subject: Re: Corrections with white matter
yes, the brainmask would be fine. The wm.mgz is to diagnose what went wrong, but the brainmask tells you whether it is right or not On Wed, 13 Jul 2011, Antonella Kis wrote:
Hi Bruce,
Thanks again for helping so much. But how about the example in the tutorial * FsTutorial/WhiteMatterEdits. I was following the example in how to fill the cutting into for yellow line. There is mentioned only to open the brainmask and wm.mgz and switching/checking between the
two
volumes. Will be this OK?
Many thanks, Antonella
_
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Sent: Wed, July 13, 2011 4:36:21 PM Subject: Re: Corrections with white matter
Hi Antonella,
you can't tell whether it is correct from overlaying it on the wm.mgz. You need to look at it over the MRI itself (either the norm.mgz or the orig.mgz) and see if you
would
have drawn it in the same place. The place where the yellow line doesn't follow the voxel surface is where a topological defect was corrected. It will be topologically correct, but possibly not geometrically so.
Bruce
On Wed, 13 Jul 2011, Antonella Kis wrote:
hi Bruce,
Sorry they are tiff. I attached them again.
Thank you very much. Antonella
_
_
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Wed, July 13, 2011 3:47:15 PM Subject: Re: Corrections with white matter
Hi Antonella,
what format are the attachments in? They don't have an extension Bruce On Wed, 13 Jul 2011, Antonella Kis wrote:
Hi Bruce,
Sorry to bother you again. I am doing my corrections for the white matter and I have few slides where I am not sure what should I do. On the slice no. 82 do I need to fill/edit voxels on the right hemisphere area where the white surface (yellow line) does not follow the surface of the brain, but in fact cuts into it 9the black
area).
Is
this a geometric inaccuracy caused by a lesion where white matter has been marked as non-white matter? I also attached the next slice no. 81 to see how things will
change.
Thank you very much for your help! Antonella
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