Hi,
I'm working with some poor quality images and having a lot of trouble with FreeSurfer segmentation. The main issue is that for a lot of images, there is a bright "strip" of hyperintense signal forming a ring around the cortex. I'm not sure what this is or where it comes from. I've attached an example image that shows where FreeSurfer has misinterpreted the GM/WM border due to this artefact. It will be quite labour intensive to manually remove the artefact, as it appears across most of the cortex.
Has anyone seen this before and/or could offer advice as to the best way to proceed? Using the 3T flag in version 5 helps a little but far from perfect.
Thanks,
Sarah
wow, that is noisy. Looks like the bright ring is dura. This isn't gado enhanced, is it? You could try using the gcut stuff
On Tue, 12 Apr 2011, Sarah Whittle wrote:
Hi,
I'm working with some poor quality images and having a lot of trouble with FreeSurfer segmentation. The main issue is that for a lot of images, there is a bright "strip" of hyperintense signal forming a ring around the cortex. I'm not sure what this is or where it comes from. I've attached an example image that shows where FreeSurfer has misinterpreted the GM/WM border due to this artefact. It will be quite labour intensive to manually remove the artefact, as it appears across most of the cortex.
Has anyone seen this before and/or could offer advice as to the best way to proceed? Using the 3T flag in version 5 helps a little but far from perfect.
Thanks,
Sarah
Thanks for your reply. I guess it could be dura. Here's a picture pre FreeSurfer with skull on. This is a particularly bad image. No, it's not gado enhanced.
gcut is automatically implemented in version 5 isn't it?? Would you suggest altering the parameters if the default doesn't help and if so, what would you suggest?
Regards,
Sarah.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, 12 April 2011 10:24 PM To: Sarah Whittle Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] hyperintense artifact causing problems for segmentation
wow, that is noisy. Looks like the bright ring is dura. This isn't gado enhanced, is it? You could try using the gcut stuff
On Tue, 12 Apr 2011, Sarah Whittle wrote:
Hi,
I'm working with some poor quality images and having a lot of trouble with FreeSurfer segmentation. The main issue is that for a lot of images, there is a bright "strip" of hyperintense signal forming a
ring
around the cortex. I'm not sure what this is or where it comes from. I've attached an example image that shows where FreeSurfer has misinterpreted the GM/WM border due to this artefact. It will be quite labour intensive to manually remove the artefact, as it appears across most of the cortex.
Has anyone seen this before and/or could offer advice as to the best
way
to proceed? Using the 3T flag in version 5 helps a little but far from perfect.
Thanks,
Sarah
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.
I'll leave that for Nick, or one of the gcut developers.
cheers Bruce On Wed, 13 Apr 2011, Sarah Whittle wrote:
Thanks for your reply. I guess it could be dura. Here's a picture pre FreeSurfer with skull on. This is a particularly bad image. No, it's not gado enhanced.
gcut is automatically implemented in version 5 isn't it?? Would you suggest altering the parameters if the default doesn't help and if so, what would you suggest?
Regards,
Sarah.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, 12 April 2011 10:24 PM To: Sarah Whittle Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] hyperintense artifact causing problems for segmentation
wow, that is noisy. Looks like the bright ring is dura. This isn't gado enhanced, is it? You could try using the gcut stuff
On Tue, 12 Apr 2011, Sarah Whittle wrote:
Hi,
I'm working with some poor quality images and having a lot of trouble with FreeSurfer segmentation. The main issue is that for a lot of images, there is a bright "strip" of hyperintense signal forming a
ring
around the cortex. I'm not sure what this is or where it comes from. I've attached an example image that shows where FreeSurfer has misinterpreted the GM/WM border due to this artefact. It will be quite labour intensive to manually remove the artefact, as it appears across most of the cortex.
Has anyone seen this before and/or could offer advice as to the best
way
to proceed? Using the 3T flag in version 5 helps a little but far from perfect.
Thanks,
Sarah
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,
Just wondering if Nick or one of the gcut developers could help me with this issue?
Regards,
Sarah
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, 13 April 2011 9:43 AM To: Sarah Whittle Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] hyperintense artifact causing problems for segmentation
I'll leave that for Nick, or one of the gcut developers.
cheers Bruce On Wed, 13 Apr 2011, Sarah Whittle wrote:
Thanks for your reply. I guess it could be dura. Here's a picture pre FreeSurfer with skull on. This is a particularly bad image. No, it's not gado enhanced.
gcut is automatically implemented in version 5 isn't it?? Would you suggest altering the parameters if the default doesn't help and if so, what would you suggest?
Regards,
Sarah.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, 12 April 2011 10:24 PM To: Sarah Whittle Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] hyperintense artifact causing problems for segmentation
wow, that is noisy. Looks like the bright ring is dura. This isn't gado enhanced, is it? You could try using the gcut stuff
On Tue, 12 Apr 2011, Sarah Whittle wrote:
Hi,
I'm working with some poor quality images and having a lot of trouble with FreeSurfer segmentation. The main issue is that for a lot of images, there is a bright "strip" of hyperintense signal forming a
ring
around the cortex. I'm not sure what this is or where it comes from. I've attached an example image that shows where FreeSurfer has misinterpreted the GM/WM border due to this artefact. It will be
quite
labour intensive to manually remove the artefact, as it appears
across
most of the cortex.
Has anyone seen this before and/or could offer advice as to the best
way
to proceed? Using the 3T flag in version 5 helps a little but far
from
perfect.
Thanks,
Sarah
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 Sarah, Nick will be out of the office until next week. I would suggest just trying to run the default gcut and if you find you need to tweak it a bit, doing mri_gcut --help will describe the parameter (-T) that you can adjust for a cleaner skullstrip. You could also run -skullstrip a second time on already stripped data to potentially get a better skullstrip. Allison
On Wed, 20 Apr 2011, Sarah Whittle wrote:
Hi,
Just wondering if Nick or one of the gcut developers could help me with this issue?
Regards,
Sarah
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, 13 April 2011 9:43 AM To: Sarah Whittle Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] hyperintense artifact causing problems for segmentation
I'll leave that for Nick, or one of the gcut developers.
cheers Bruce On Wed, 13 Apr 2011, Sarah Whittle wrote:
Thanks for your reply. I guess it could be dura. Here's a picture pre FreeSurfer with skull on. This is a particularly bad image. No, it's not gado enhanced.
gcut is automatically implemented in version 5 isn't it?? Would you suggest altering the parameters if the default doesn't help and if so, what would you suggest?
Regards,
Sarah.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, 12 April 2011 10:24 PM To: Sarah Whittle Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] hyperintense artifact causing problems for segmentation
wow, that is noisy. Looks like the bright ring is dura. This isn't gado enhanced, is it? You could try using the gcut stuff
On Tue, 12 Apr 2011, Sarah Whittle wrote:
Hi,
I'm working with some poor quality images and having a lot of trouble with FreeSurfer segmentation. The main issue is that for a lot of images, there is a bright "strip" of hyperintense signal forming a
ring
around the cortex. I'm not sure what this is or where it comes from. I've attached an example image that shows where FreeSurfer has misinterpreted the GM/WM border due to this artefact. It will be
quite
labour intensive to manually remove the artefact, as it appears
across
most of the cortex.
Has anyone seen this before and/or could offer advice as to the best
way
to proceed? Using the 3T flag in version 5 helps a little but far
from
perfect.
Thanks,
Sarah
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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