Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit.
Thank you Allison and Bruce for your feedback!
Some follow-up questions if I may - are the volumes for the gray matter and the cerebellum as indicated in the aseg stats file reliable and thus usable (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use the cerebellum volume if it's labeled as GM)? If not how should we rectify this, and at which point must that be done (I've already gone ahead and begun recon3 without editing - can this be fixed post-recon3?)? Please let me know what you think.
Thank you once again in advance - Happy Labor Day weekend!
Miyoung
-----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 12:06 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Hi Miyoung,
you can always edit the aseg.mgz if you want. Do you find this happens frequently? That hasn't been our experience. Bruce On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Thank you Allison and Bruce for your feedback!
Some follow-up questions if I may - are the volumes for the gray matter and the cerebellum as indicated in the aseg stats file reliable and thus usable (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use the cerebellum volume if it's labeled as GM)? If not how should we rectify this, and at which point must that be done (I've already gone ahead and begun recon3 without editing - can this be fixed post-recon3?)? Please let me know what you think.
Thank you once again in advance - Happy Labor Day weekend!
Miyoung
-----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 12:06 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Bruce.
Thanks for your reply - it appears that this has happened before (though I'm not exactly certain how often) and we suspect it could happen again in the future. You mentioned editing the aseg.mgz - would you point us to the place on the Wiki page that details how this is done and also, can the editing be accomplished without compromising the global GM/cerebellar/etc. volumes significantly? Please let us know what you think. Thanks in advance!!
Miyoung
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 7:28 PM To: Kim, Miyoung Cc: Allison Stevens; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
Hi Miyoung,
you can always edit the aseg.mgz if you want. Do you find this happens frequently? That hasn't been our experience. Bruce On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Thank you Allison and Bruce for your feedback!
Some follow-up questions if I may - are the volumes for the gray matter and the cerebellum as indicated in the aseg stats file reliable and thus usable (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use the cerebellum volume if it's labeled as GM)? If not how should we rectify this, and at which point must that be done (I've already gone ahead and begun recon3 without editing - can this be fixed post-recon3?)? Please let me know what you think.
Thank you once again in advance - Happy Labor Day weekend!
Miyoung
-----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 12:06 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Hi.
I wasn't sure if my previous email (below) went through - essentially we have a cortical occipital area that Freesurfer, upon segmentation, labels it as cerebellum even though the pial surface appears to have been outlined correctly (happened twice on the same data!) - I was under the impression from the responses that the parcellation is performed using the surfaces so I went ahead to recon3 - unfortunately that part of the cortex is still labeled as cerebellum (see attached).
One of my colleagues told me that she saw instances where the pial surface would cut into the cerebellum - can editing the aseg.mgz fix both issues? If so would you please direct me to the place on the Wiki page that details this process (sorry - I wasn't able to find it)? Thanks much in advance!!
Miyoung
-----Original Message----- From: Kim, Miyoung Sent: Tuesday, September 08, 2009 2:16 PM To: 'Bruce Fischl' Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject)
Hi, Bruce.
Thanks for your reply - it appears that this has happened before (though I'm not exactly certain how often) and we suspect it could happen again in the future. You mentioned editing the aseg.mgz - would you point us to the place on the Wiki page that details how this is done and also, can the editing be accomplished without compromising the global GM/cerebellar/etc. volumes significantly? Please let us know what you think. Thanks in advance!!
Miyoung
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 7:28 PM To: Kim, Miyoung Cc: Allison Stevens; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
Hi Miyoung,
you can always edit the aseg.mgz if you want. Do you find this happens frequently? That hasn't been our experience. Bruce On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Thank you Allison and Bruce for your feedback!
Some follow-up questions if I may - are the volumes for the gray matter and the cerebellum as indicated in the aseg stats file reliable and thus usable (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use the cerebellum volume if it's labeled as GM)? If not how should we rectify this, and at which point must that be done (I've already gone ahead and begun recon3 without editing - can this be fixed post-recon3?)? Please let me know what you think.
Thank you once again in advance - Happy Labor Day weekend!
Miyoung
-----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 12:06 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Does it look that way on the aparc+aseg.mgz?
Kim, Miyoung wrote:
Hi.
I wasn't sure if my previous email (below) went through - essentially we have a cortical occipital area that Freesurfer, upon segmentation, labels it as cerebellum even though the pial surface appears to have been outlined correctly (happened twice on the same data!) - I was under the impression from the responses that the parcellation is performed using the surfaces so I went ahead to recon3 - unfortunately that part of the cortex is still labeled as cerebellum (see attached).
One of my colleagues told me that she saw instances where the pial surface would cut into the cerebellum - can editing the aseg.mgz fix both issues? If so would you please direct me to the place on the Wiki page that details this process (sorry - I wasn't able to find it)? Thanks much in advance!!
Miyoung
-----Original Message----- From: Kim, Miyoung Sent: Tuesday, September 08, 2009 2:16 PM To: 'Bruce Fischl' Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject)
Hi, Bruce.
Thanks for your reply - it appears that this has happened before (though I'm not exactly certain how often) and we suspect it could happen again in the future. You mentioned editing the aseg.mgz - would you point us to the place on the Wiki page that details how this is done and also, can the editing be accomplished without compromising the global GM/cerebellar/etc. volumes significantly? Please let us know what you think. Thanks in advance!!
Miyoung
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 7:28 PM To: Kim, Miyoung Cc: Allison Stevens; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
Hi Miyoung,
you can always edit the aseg.mgz if you want. Do you find this happens frequently? That hasn't been our experience. Bruce On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Thank you Allison and Bruce for your feedback!
Some follow-up questions if I may - are the volumes for the gray matter and the cerebellum as indicated in the aseg stats file reliable and thus usable (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use the cerebellum volume if it's labeled as GM)? If not how should we rectify this, and at which point must that be done (I've already gone ahead and begun recon3 without editing - can this be fixed post-recon3?)? Please let me know what you think.
Thank you once again in advance - Happy Labor Day weekend!
Miyoung
-----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 12:06 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Doug.
It is the output after autorecon3 (so yes, aparc+aseg.mgz).....
I found another situation similar to this (different subject) - see attached. It seems like it might be occurring more frequently than I had suspected earlier.
Miyoung
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, September 10, 2009 4:16 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] editing aseg.mgz?
Does it look that way on the aparc+aseg.mgz?
Kim, Miyoung wrote:
Hi.
I wasn't sure if my previous email (below) went through - essentially we have a cortical occipital area that Freesurfer, upon segmentation, labels it as cerebellum even though the pial surface appears to have been outlined correctly (happened twice on the same data!) - I was under the impression from the responses that the parcellation is performed using the surfaces so I went ahead to recon3 - unfortunately that part of the cortex is still labeled as cerebellum (see attached).
One of my colleagues told me that she saw instances where the pial surface would cut into the cerebellum - can editing the aseg.mgz fix both issues? If so would you please direct me to the place on the Wiki page that details this process (sorry - I wasn't able to find it)? Thanks much in advance!!
Miyoung
-----Original Message----- From: Kim, Miyoung Sent: Tuesday, September 08, 2009 2:16 PM To: 'Bruce Fischl' Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject)
Hi, Bruce.
Thanks for your reply - it appears that this has happened before (though I'm not exactly certain how often) and we suspect it could happen again in the future. You mentioned editing the aseg.mgz - would you point us to the place on the Wiki page that details how this is done and also, can the editing be accomplished without compromising the global GM/cerebellar/etc. volumes significantly? Please let us know what you think. Thanks in advance!!
Miyoung
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 7:28 PM To: Kim, Miyoung Cc: Allison Stevens; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
Hi Miyoung,
you can always edit the aseg.mgz if you want. Do you find this happens frequently? That hasn't been our experience. Bruce On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Thank you Allison and Bruce for your feedback!
Some follow-up questions if I may - are the volumes for the gray matter and the cerebellum as indicated in the aseg stats file reliable and thus usable (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use the cerebellum volume if it's labeled as GM)? If not how should we rectify this, and at which point must that be done (I've already gone ahead and begun recon3 without editing - can this be fixed post-recon3?)? Please let me know what you think.
Thank you once again in advance - Happy Labor Day weekend!
Miyoung
-----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 12:06 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
hmmm, I guess the ribbons should override the aseg w.r.t. cerebellum label as well.
On Fri, 11 Sep 2009, Kim, Miyoung wrote:
Hi, Doug.
It is the output after autorecon3 (so yes, aparc+aseg.mgz).....
I found another situation similar to this (different subject) - see attached. It seems like it might be occurring more frequently than I had suspected earlier.
Miyoung
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, September 10, 2009 4:16 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] editing aseg.mgz?
Does it look that way on the aparc+aseg.mgz?
Kim, Miyoung wrote:
Hi.
I wasn't sure if my previous email (below) went through - essentially we have a cortical occipital area that Freesurfer, upon segmentation, labels it as cerebellum even though the pial surface appears to have been outlined correctly (happened twice on the same data!) - I was under the impression from the responses that the parcellation is performed using the surfaces so I went ahead to recon3 - unfortunately that part of the cortex is still labeled as cerebellum (see attached).
One of my colleagues told me that she saw instances where the pial surface would cut into the cerebellum - can editing the aseg.mgz fix both issues? If so would you please direct me to the place on the Wiki page that details this process (sorry - I wasn't able to find it)? Thanks much in advance!!
Miyoung
-----Original Message----- From: Kim, Miyoung Sent: Tuesday, September 08, 2009 2:16 PM To: 'Bruce Fischl' Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject)
Hi, Bruce.
Thanks for your reply - it appears that this has happened before (though I'm not exactly certain how often) and we suspect it could happen again in the future. You mentioned editing the aseg.mgz - would you point us to the place on the Wiki page that details how this is done and also, can the editing be accomplished without compromising the global GM/cerebellar/etc. volumes significantly? Please let us know what you think. Thanks in advance!!
Miyoung
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 7:28 PM To: Kim, Miyoung Cc: Allison Stevens; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
Hi Miyoung,
you can always edit the aseg.mgz if you want. Do you find this happens frequently? That hasn't been our experience. Bruce On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Thank you Allison and Bruce for your feedback!
Some follow-up questions if I may - are the volumes for the gray matter and the cerebellum as indicated in the aseg stats file reliable and thus usable (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use the cerebellum volume if it's labeled as GM)? If not how should we rectify this, and at which point must that be done (I've already gone ahead and begun recon3 without editing - can this be fixed post-recon3?)? Please let me know what you think.
Thank you once again in advance - Happy Labor Day weekend!
Miyoung
-----Original Message----- From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Friday, September 04, 2009 12:06 PM To: Kim, Miyoung Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit.
--
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
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Hi Miyoung",
it's based on the white (yellow line) and pial surfaces.
cheers, Bruce
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
So the segmentation and the cortical parcellation are completely independent? Or does the cortical parcellation still use information from the segmentation?
Bruce Fischl wrote:
Hi Miyoung",
it's based on the white (yellow line) and pial surfaces.
cheers, Bruce
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
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Hi Anthony,
mostly independent. The surface reconstruction itself is dependent on the subcortical labeling, and we do use the subcortical information for distinguishing callosum for cingulate and such, but otherwise they are independent.
cheers, Bruce On Fri, 4 Sep 2009, Anthony Dick wrote:
So the segmentation and the cortical parcellation are completely independent? Or does the cortical parcellation still use information from the segmentation?
Bruce Fischl wrote:
Hi Miyoung",
it's based on the white (yellow line) and pial surfaces.
cheers, Bruce
On Fri, 4 Sep 2009, Kim, Miyoung wrote:
Hi.
Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance!
Miyoung
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
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Kim, Miyoung