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 <fis...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@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 <fis...@nmr.mgh.harvard.edu>
> To: Antonella Kis <ator...@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 <fis...@nmr.mgh.harvard.edu>
> > To: Antonella Kis <ator...@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
> > >
> > >
> > >
> > >
> >
> >
> > The information in this e-mail is intended only for the person to whom it is
> > addressed. If you believe this e-mail was sent to you in error and the
e-mail
> > contains patient information, please contact the Partners Compliance
HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you in
error
> > but does not contain patient information, please contact the sender and
properly
> > dispose of the e-mail.
> >
> >
>
>
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