Hi,
I am part of a group interested in measuring cortical thickness and we have had problems with skull stripping. We read on the mailing list that you are not supposed to delete the skull with the edit voxel tool on the brainmask.mgz because it affects the surfaces. What would be an appropriate way to delete/remove the skull? We tried lowering the watershed threshold (normally at 5) to 3, and found skull still being classified as brain as well as some brain missing.
Thank you, I look forward to hearing your response.
Sincerely,
Athena
Hi Athena,
Small pieces of skull left is fine as long as the surfaces look okay. But if they don't or if you want to edit the skull for any other reason, you can do it manually but be careful not to edit the grey matter, which will affect the surfaces. If there is a large chunk of skull remaining or brain missing, you are better off using the automated procedures to save time instead of the manual edits. To remove the skull, try different values for the watershed threshold (20, 15, 10 etc..)
Please refer to this wiki for more info. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
Sita.
On Wed, 6 May 2009, Drosos, Athena wrote:
Hi,
I am part of a group interested in measuring cortical thickness and we have had problems with skull stripping. We read on the mailing list that you are not supposed to delete the skull with the edit voxel tool on the brainmask.mgz because it affects the surfaces. What would be an appropriate way to delete/remove the skull? We tried lowering the watershed threshold (normally at 5) to 3, and found skull still being classified as brain as well as some brain missing.
Thank you, I look forward to hearing your response.
Sincerely,
Athena
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Sita,
Thank you for your response. Our problem is that skull is being classified as grey matter, which affects our cortical thickness measures. We ended up doing manual edits to the brainmask volume for our subjects and rerunning autorecon2 with the wm flag. This has worked on some subjects, but on others we have been getting this error:
#@# Fix Topology lh Wed May 6 17:57:58 EDT 2009 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n cp: ../surf/lh.inflated: Permission denied
Any suggestions on how to go about fixing this?
Thank you in advance,
Athena
On 5/6/09 7:14 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
Hi Athena,
Small pieces of skull left is fine as long as the surfaces look okay. But if they don't or if you want to edit the skull for any other reason, you can do it manually but be careful not to edit the grey matter, which will affect the surfaces. If there is a large chunk of skull remaining or brain missing, you are better off using the automated procedures to save time instead of the manual edits. To remove the skull, try different values for the watershed threshold (20, 15, 10 etc..)
Please refer to this wiki for more info. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
Sita.
On Wed, 6 May 2009, Drosos, Athena wrote:
Hi,
I am part of a group interested in measuring cortical thickness and we have had problems with skull stripping. We read on the mailing list that you are not supposed to delete the skull with the edit voxel tool on the brainmask.mgz because it affects the surfaces. What would be an appropriate way to delete/remove the skull? We tried lowering the watershed threshold (normally at 5) to 3, and found skull still being classified as brain as well as some brain missing.
Thank you, I look forward to hearing your response.
Sincerely,
Athena
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Athena Drosos Research Assistant P.A.I.N. Group Radiology Department Children's Hospital Boston at Waltham 9 Hope Ave Waltham, MA 02453 Lab Phone: 781-216-1199
it is classified as GM in the aseg, or does the pial surface include it? If the former then it doesn't really matter, but if the pial grabs it you need to edit it.
cheers, Bruce
On Thu, 7 May 2009, Drosos, Athena wrote:
Hi Sita,
Thank you for your response. Our problem is that skull is being classified as grey matter, which affects our cortical thickness measures. We ended up doing manual edits to the brainmask volume for our subjects and rerunning autorecon2 with the wm flag. This has worked on some subjects, but on others we have been getting this error:
#@# Fix Topology lh Wed May 6 17:57:58 EDT 2009 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n cp: ../surf/lh.inflated: Permission denied
Any suggestions on how to go about fixing this?
Thank you in advance,
Athena
On 5/6/09 7:14 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
Hi Athena,
Small pieces of skull left is fine as long as the surfaces look okay. But if they don't or if you want to edit the skull for any other reason, you can do it manually but be careful not to edit the grey matter, which will affect the surfaces. If there is a large chunk of skull remaining or brain missing, you are better off using the automated procedures to save time instead of the manual edits. To remove the skull, try different values for the watershed threshold (20, 15, 10 etc..)
Please refer to this wiki for more info. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
Sita.
On Wed, 6 May 2009, Drosos, Athena wrote:
Hi,
I am part of a group interested in measuring cortical thickness and we have had problems with skull stripping. We read on the mailing list that you are not supposed to delete the skull with the edit voxel tool on the brainmask.mgz because it affects the surfaces. What would be an appropriate way to delete/remove the skull? We tried lowering the watershed threshold (normally at 5) to 3, and found skull still being classified as brain as well as some brain missing.
Thank you, I look forward to hearing your response.
Sincerely,
Athena
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Athena Drosos Research Assistant P.A.I.N. Group Radiology Department Children's Hospital Boston at Waltham 9 Hope Ave Waltham, MA 02453 Lab Phone: 781-216-1199
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Drosos, Athena -
Sita Kakunoori