Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0. My questions are 1) Do you have any additional suggestion to fix this bug? 2) If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
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one more question: I replace the mislabeled lateral ventricle with CSF because I can not find the "none" in the FreesurfercolorLUT.txt. How to change the mislabeled lateral ventricle to none?
Thank you,
Xin
________________________________
From: Wang, Xin Sent: Thu 10/7/2010 12:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: zero cortical thickness in the lingual and precuneus
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0. My questions are 1) Do you have any additional suggestion to fix this bug? 2) If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
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You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
None should be the first label in the FreeSurferColorLUT.txt (it's labeled as "Unknown" with an ID# of 0). But really you should be labeling it what it truly is. Is this the gray matter you are labeling as CSF?
Thank you, Allison. Is Unknown for the empty space between gyri? I did label the gray matter vertices as cortex.
Xin
________________________________
From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Thu 10/7/2010 12:16 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus
None should be the first label in the FreeSurferColorLUT.txt (it's labeled as "Unknown" with an ID# of 0). But really you should be labeling it what it truly is. Is this the gray matter you are labeling as CSF?
--
On Thu, 7 Oct 2010, Wang, Xin wrote:
one more question: I replace the mislabeled lateral ventricle with CSF because I can not find the "none" in the FreesurfercolorLUT.txt. How to change the mislabeled lateral ventricle to none?
Thank you,
Xin
From: Wang, Xin Sent: Thu 10/7/2010 12:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: zero cortical thickness in the lingual and precuneus
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0. My questions are
- Do you have any additional suggestion to fix this bug?
- If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
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.
yes it is On Thu, 7 Oct 2010, Wang, Xin wrote:
Thank you, Allison. Is Unknown for the empty space between gyri? I did label the gray matter vertices as cortex.
Xin
From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Thu 10/7/2010 12:16 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus
None should be the first label in the FreeSurferColorLUT.txt (it's labeled as "Unknown" with an ID# of 0). But really you should be labeling it what it truly is. Is this the gray matter you are labeling as CSF?
--
On Thu, 7 Oct 2010, Wang, Xin wrote:
one more question: I replace the mislabeled lateral ventricle with CSF because I can not find the "none" in the FreesurfercolorLUT.txt. How to change the mislabeled lateral ventricle to none?
Thank you,
Xin
From: Wang, Xin Sent: Thu 10/7/2010 12:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: zero cortical thickness in the lingual and precuneus
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0. My questions are
- Do you have any additional suggestion to fix this bug?
- If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
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.
set it to "Unknown" which is 0 On Thu, 7 Oct 2010, Wang, Xin wrote:
one more question: I replace the mislabeled lateral ventricle with CSF because I can not find the "none" in the FreesurfercolorLUT.txt. How to change the mislabeled lateral ventricle to none?
Thank you,
Xin
From: Wang, Xin Sent: Thu 10/7/2010 12:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: zero cortical thickness in the lingual and precuneus
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0. My questions are
- Do you have any additional suggestion to fix this bug?
- If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Hi Xin,
can you upload this dataset so we can take a look?
Bruce On Thu, 7 Oct 2010, Wang, Xin wrote:
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the
lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0.
My questions are
- Do you have any additional suggestion to fix this bug?
- If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Thank you, Dr. Fischl. I will try another round of correction, and please instruct me how to upload a subject data to your workstation? so we can look into this problem at same time.
Xin
________________________________
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 10/7/2010 12:17 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus
Hi Xin,
can you upload this dataset so we can take a look?
Bruce On Thu, 7 Oct 2010, Wang, Xin wrote:
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the
lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0.
My questions are
- Do you have any additional suggestion to fix this bug?
- If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
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.
you can find it on our wiki On Thu, 7 Oct 2010, Wang, Xin wrote:
Thank you, Dr. Fischl. I will try another round of correction, and please instruct me how to upload a subject data to your workstation? so we can look into this problem at same time.
Xin
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 10/7/2010 12:17 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus
Hi Xin,
can you upload this dataset so we can take a look?
Bruce On Thu, 7 Oct 2010, Wang, Xin wrote:
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the
lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0.
My questions are
- Do you have any additional suggestion to fix this bug?
- If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
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.
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
use the Upload button.
On Thu, 2010-10-07 at 12:25 -0400, Wang, Xin wrote:
Thank you, Dr. Fischl. I will try another round of correction, and please instruct me how to upload a subject data to your workstation? so we can look into this problem at same time.
Xin
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 10/7/2010 12:17 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus
Hi Xin,
can you upload this dataset so we can take a look?
Bruce On Thu, 7 Oct 2010, Wang, Xin wrote:
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the
lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0.
My questions are
- Do you have any additional suggestion to fix this bug?
- If not, do you have a way to exclude this problematic sulcus? In
another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
freesurfer-request@nmr.mgh.harvard.edu
Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
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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Nick Schmansky -
Wang, Xin