Hi all,
I would love information on how best to tackle and alleviate this type of surface issue. Images attached.
Hi Jon
that is almost certainly a topology correction problem. Check to see if the wm.mgz contains any spurious connections that cause the space that is missing in the ?h.white surface to be closed in a slice. If you upload the data we can show you how to correct it if you want.
cheers Bruce On Fri, 25 Apr 2014, Jonathan Holt wrote:
Hi all, I would love information on how best to tackle and alleviate this type of surface issue. Images attached.
Thanks Bruce,
I’ll check for such wm connections. Is this the default method for correcting topology issues?
jon On Apr 25, 2014, at 10:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
that is almost certainly a topology correction problem. Check to see if the wm.mgz contains any spurious connections that cause the space that is missing in the ?h.white surface to be closed in a slice. If you upload the data we can show you how to correct it if you want.
cheers Bruce On Fri, 25 Apr 2014, Jonathan Holt wrote:
Hi all, I would love information on how best to tackle and alleviate this type of surface issue. Images attached.
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.
Hi Jon
in this kind of case the default method did the wrong thing (closing the hole instead of cutting the handle). You need to identify the incorrectly segmented voxels that cause the spurious correction and delete them from the wm.mgz, then run autorecon2-wm autorecon3
cheers Bruce
On Fri, 25 Apr 2014, Jonathan Holt wrote:
Thanks Bruce,
I’ll check for such wm connections. Is this the default method for correcting topology issues?
jon On Apr 25, 2014, at 10:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
that is almost certainly a topology correction problem. Check to see if the wm.mgz contains any spurious connections that cause the space that is missing in the ?h.white surface to be closed in a slice. If you upload the data we can show you how to correct it if you want.
cheers Bruce On Fri, 25 Apr 2014, Jonathan Holt wrote:
Hi all, I would love information on how best to tackle and alleviate this type of surface issue. Images attached.
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bruce,
I dont see any WM connections that jump out at me. Could I upload it and have a second opinion?
Jon On Apr 25, 2014, at 11:33 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
in this kind of case the default method did the wrong thing (closing the hole instead of cutting the handle). You need to identify the incorrectly segmented voxels that cause the spurious correction and delete them from the wm.mgz, then run autorecon2-wm autorecon3
cheers Bruce
On Fri, 25 Apr 2014, Jonathan Holt wrote:
Thanks Bruce,
I’ll check for such wm connections. Is this the default method for correcting topology issues?
jon On Apr 25, 2014, at 10:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
that is almost certainly a topology correction problem. Check to see if the wm.mgz contains any spurious connections that cause the space that is missing in the ?h.white surface to be closed in a slice. If you upload the data we can show you how to correct it if you want.
cheers Bruce On Fri, 25 Apr 2014, Jonathan Holt wrote:
Hi all, I would love information on how best to tackle and alleviate this type of surface issue. Images attached.
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 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.
sure On Mon, 28 Apr 2014, Jonathan Holt wrote:
Bruce,
I dont see any WM connections that jump out at me. Could I upload it and have a second opinion?
Jon On Apr 25, 2014, at 11:33 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
in this kind of case the default method did the wrong thing (closing the hole instead of cutting the handle). You need to identify the incorrectly segmented voxels that cause the spurious correction and delete them from the wm.mgz, then run autorecon2-wm autorecon3
cheers Bruce
On Fri, 25 Apr 2014, Jonathan Holt wrote:
Thanks Bruce,
I’ll check for such wm connections. Is this the default method for correcting topology issues?
jon On Apr 25, 2014, at 10:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
that is almost certainly a topology correction problem. Check to see if the wm.mgz contains any spurious connections that cause the space that is missing in the ?h.white surface to be closed in a slice. If you upload the data we can show you how to correct it if you want.
cheers Bruce On Fri, 25 Apr 2014, Jonathan Holt wrote:
Hi all, I would love information on how best to tackle and alleviate this type of surface issue. Images attached.
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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Look for spuriousWMconnections.tar
jon On Apr 28, 2014, at 12:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
sure On Mon, 28 Apr 2014, Jonathan Holt wrote:
Bruce,
I dont see any WM connections that jump out at me. Could I upload it and have a second opinion?
Jon On Apr 25, 2014, at 11:33 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
in this kind of case the default method did the wrong thing (closing the hole instead of cutting the handle). You need to identify the incorrectly segmented voxels that cause the spurious correction and delete them from the wm.mgz, then run autorecon2-wm autorecon3
cheers Bruce
On Fri, 25 Apr 2014, Jonathan Holt wrote:
Thanks Bruce,
I’ll check for such wm connections. Is this the default method for correcting topology issues?
jon On Apr 25, 2014, at 10:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jon
that is almost certainly a topology correction problem. Check to see if the wm.mgz contains any spurious connections that cause the space that is missing in the ?h.white surface to be closed in a slice. If you upload the data we can show you how to correct it if you want.
cheers Bruce On Fri, 25 Apr 2014, Jonathan Holt wrote:
Hi all, I would love information on how best to tackle and alleviate this type of surface issue. Images attached.
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 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 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
-
Bruce Fischl -
Jonathan Holt