Dear list,
we are experiencing a strange wm surface error that we are not quite sure about how to fix. The errors is at a location where the wm.mgz look absolutely fine as well as the brainmask.mgz. Also the intensities in the norm.mgz look fine.
Please find 6 pics showing the error highlighted by the cursor on the brainmask.mgz and the wm.mgz in all three views.
Cheers, Mel
Hi Mel, how does the orig or orig.nofix look?
On 2/24/17 9:21 AM, Melanie Ganz wrote:
Dear list,
we are experiencing a strange wm surface error that we are not quite sure about how to fix. The errors is at a location where the wm.mgz look absolutely fine as well as the brainmask.mgz. Also the intensities in the norm.mgz look fine.
Please find 6 pics showing the error highlighted by the cursor on the brainmask.mgz and the wm.mgz in all three views.
Cheers, Mel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
the orig looks fine and we cannot see a file orig.nofix in the subject dirs. We still use v5.3.
But what we tried now for another similar subject was to remove falsely labelled white matter in dura which was far away, but that fixed the white matter errors so far inside the brain. Does that make any sense to you why that helps?
Cheers, Mel
On 27-02-2017 5:23, Douglas Greve wrote:
Hi Mel, how does the orig or orig.nofix look?
On 2/24/17 9:21 AM, Melanie Ganz wrote:
Dear list,
we are experiencing a strange wm surface error that we are not quite sure about how to fix. The errors is at a location where the wm.mgz look absolutely fine as well as the brainmask.mgz. Also the intensities in the norm.mgz look fine.
Please find 6 pics showing the error highlighted by the cursor on the brainmask.mgz and the wm.mgz in all three views.
Cheers, Mel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
That does not make sense. Can you run this subject in v6? If the problem goes away, then there is not much we can do about it in 5.3
On 02/28/2017 05:27 AM, Melanie Ganz wrote:
Hi Doug,
the orig looks fine and we cannot see a file orig.nofix in the subject dirs. We still use v5.3.
But what we tried now for another similar subject was to remove falsely labelled white matter in dura which was far away, but that fixed the white matter errors so far inside the brain. Does that make any sense to you why that helps?
Cheers, Mel
On 27-02-2017 5:23, Douglas Greve wrote:
Hi Mel, how does the orig or orig.nofix look?
On 2/24/17 9:21 AM, Melanie Ganz wrote:
Dear list,
we are experiencing a strange wm surface error that we are not quite sure about how to fix. The errors is at a location where the wm.mgz look absolutely fine as well as the brainmask.mgz. Also the intensities in the norm.mgz look fine.
Please find 6 pics showing the error highlighted by the cursor on the brainmask.mgz and the wm.mgz in all three views.
Cheers, Mel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark
phone: +45 3545 6718 e-mail:Melanie.Ganz@nru.dk web:http://melanie.clausundmelanie.de/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry for the delayed response. it makes sense *if* the ?h.orig.nofix surface contains those voxels
cheers Bruce
On Tue, 28 Feb 2017, Melanie Ganz wrote:
Hi Doug,
the orig looks fine and we cannot see a file orig.nofix in the subject dirs. We still use v5.3.
But what we tried now for another similar subject was to remove falsely labelled white matter in dura which was far away, but that fixed the white matter errors so far inside the brain. Does that make any sense to you why that helps?
Cheers, Mel
On 27-02-2017 5:23, Douglas Greve wrote:
Hi Mel, how does the orig or orig.nofix look? On 2/24/17 9:21 AM, Melanie Ganz wrote: Dear list, we are experiencing a strange wm surface error that we are not quite sure about how to fix. The errors is at a location where the wm.mgz look absolutely fine as well as the brainmask.mgz. Also the intensities in the norm.mgz look fine. Please find 6 pics showing the error highlighted by the cursor on the brainmask.mgz and the wm.mgz in all three views. Cheers, Mel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Melanie Ganz