FS experts,
Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas?
I fear it may believe they are dura because of the similar intensity values.
jon
why are they so bright? Are they that way before intensity normalization (e.g. in the orig.mgz)? On Mon, 21 Oct 2013, Jonathan Holt wrote:
FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas?
I fear it may believe they are dura because of the similar intensity values.
jon
They are bright in orig.mgz. You can see in the pictured attachments
On Mon, Oct 21, 2013 at 1:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
why are they so bright? Are they that way before intensity normalization (e.g. in the orig.mgz)?
On Mon, 21 Oct 2013, Jonathan Holt wrote:
FS experts,
Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas?
I fear it may believe they are dura because of the similar intensity values.
jon
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/**compliancelinehttp://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.
I'm not sure it's fixable then. Any idea what they are? Bruce
On Oct 22, 2013, at 9:30 AM, Jonathan Holt whatsdac@umich.edu wrote:
They are bright in orig.mgz. You can see in the pictured attachments
On Mon, Oct 21, 2013 at 1:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: why are they so bright? Are they that way before intensity normalization (e.g. in the orig.mgz)?
On Mon, 21 Oct 2013, Jonathan Holt wrote:
FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas?
I fear it may believe they are dura because of the similar intensity values.
jon
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.
<Screen Shot 2013-10-21 at 2.01.00 PM.png> <Screen Shot 2013-10-21 at 2.00.45 PM.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
No, you mean anatomically speaking? If it's unfixable then that's OK, was just wondering if it was possible.
On Oct 22, 2013, at 10:14 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I'm not sure it's fixable then. Any idea what they are? Bruce
On Oct 22, 2013, at 9:30 AM, Jonathan Holt whatsdac@umich.edu wrote:
They are bright in orig.mgz. You can see in the pictured attachments
On Mon, Oct 21, 2013 at 1:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: why are they so bright? Are they that way before intensity normalization (e.g. in the orig.mgz)?
On Mon, 21 Oct 2013, Jonathan Holt wrote:
FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas?
I fear it may believe they are dura because of the similar intensity values.
jon
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.
<Screen Shot 2013-10-21 at 2.01.00 PM.png> <Screen Shot 2013-10-21 at 2.00.45 PM.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, anatomically. And I would guess it's unfixable without tons of work On Wed, 23 Oct 2013, Jon Holt wrote:
No, you mean anatomically speaking? If it's unfixable then that's OK, was just wondering if it was possible.
On Oct 22, 2013, at 10:14 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I'm not sure it's fixable then. Any idea what they are?Bruce
On Oct 22, 2013, at 9:30 AM, Jonathan Holt whatsdac@umich.edu wrote:
They are bright in orig.mgz. You can see in the pictured attachmentsOn Mon, Oct 21, 2013 at 1:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: why are they so bright? Are they that way before intensity normalization (e.g. in the orig.mgz)? On Mon, 21 Oct 2013, Jonathan Holt wrote:
FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas? I fear it may believe they are dura because of the similar intensity values. jonThe 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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