Hi,
Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of "testingfreesurfer".
"...... Found embedded color table in annotation. 8600 vertices did not have an annotation!"
What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation & surface ) or my computer system? Is it normal to get it?
Thanks a lot
Jerry
________________________________
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Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug
Chen, Xu wrote:
Hi,
Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of "testingfreesurfer".
"...... Found embedded color table in annotation. 8600 vertices did not have an annotation!"
What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation & surface ) or my computer system? Is it normal to get it?
Thanks a lot
Jerry
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Doug
As instructed in the testing page, I typed "tksurfer bert rh pial" and then went to File->Label->Import Annotation. The file rh.aparc.annot was selected to view cortical parcellation labels.
Thanks Jerry ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 11:28 AM To: Chen, Xu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug
Chen, Xu wrote:
Hi,
Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of "testingfreesurfer".
"...... Found embedded color table in annotation. 8600 vertices did not have an annotation!"
What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation & surface ) or my computer system? Is it normal to get it?
Thanks a lot
Jerry
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 Jerry
were these just the locations on the medial wall around the corpus callosum that are non-cortical?
cheers Bruce On Mon, 19 Sep 2011, Chen, Xu wrote:
Hi, Doug
As instructed in the testing page, I typed "tksurfer bert rh pial" and then went to File->Label->Import Annotation. The file rh.aparc.annot was selected to view cortical parcellation labels.
Thanks Jerry ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 11:28 AM To: Chen, Xu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug
Chen, Xu wrote:
Hi,
Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of "testingfreesurfer".
"...... Found embedded color table in annotation. 8600 vertices did not have an annotation!"
What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation & surface ) or my computer system? Is it normal to get it?
Thanks a lot
Jerry
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
Yes, that message is that the medial all vertices do not have a label. This is normal and nothing to worry about. doug
Bruce Fischl wrote:
Hi Jerry
were these just the locations on the medial wall around the corpus callosum that are non-cortical?
cheers Bruce On Mon, 19 Sep 2011, Chen, Xu wrote:
Hi, Doug
As instructed in the testing page, I typed "tksurfer bert rh pial" and then went to File->Label->Import Annotation. The file rh.aparc.annot was selected to view cortical parcellation labels.
Thanks Jerry ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 11:28 AM To: Chen, Xu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug
Chen, Xu wrote:
Hi,
Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of "testingfreesurfer".
"...... Found embedded color table in annotation. 8600 vertices did not have an annotation!"
What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation & surface ) or my computer system? Is it normal to get it?
Thanks a lot
Jerry
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
Thanks for the clarification! Cheers
Jerry ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, September 19, 2011 10:15 AM To: Bruce Fischl Cc: Chen, Xu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Yes, that message is that the medial all vertices do not have a label. This is normal and nothing to worry about. doug
Bruce Fischl wrote:
Hi Jerry
were these just the locations on the medial wall around the corpus callosum that are non-cortical?
cheers Bruce On Mon, 19 Sep 2011, Chen, Xu wrote:
Hi, Doug
As instructed in the testing page, I typed "tksurfer bert rh pial" and then went to File->Label->Import Annotation. The file rh.aparc.annot was selected to view cortical parcellation labels.
Thanks Jerry ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 11:28 AM To: Chen, Xu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Is this normal when importing the annotations in tksurfer?
Hi Jerry, what is the command you are running? I mean the full command line including the arguments. doug
Chen, Xu wrote:
Hi,
Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of "testingfreesurfer".
"...... Found embedded color table in annotation. 8600 vertices did not have an annotation!"
What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation & surface ) or my computer system? Is it normal to get it?
Thanks a lot
Jerry
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Chen, Xu -
Douglas N Greve