Dear All,
After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes.
Regards Ayaz
The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
Hi Ayaz
what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2)
cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote:
Dear All,
After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV.
Any suggestions? I need to calculate normalized volumes.
Regards
Ayaz
The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
Well, I am using version 5.1.0. I have had same issue in fewer subjects when I used the older version as well. Any comments about that?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all
Hi Ayaz
what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2)
cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote:
Dear All,
After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV.
Any suggestions? I need to calculate normalized volumes.
Regards
Ayaz
The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
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.
The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
can you send us an example? In the ones we've looked at the older versions were more stable. Alternatively, we can send you a new template that Avi Snyder generated that you could try out
cheers Bruce
On Mon, 16 Jul 2012, Ayaz, Muhammad wrote:
Well, I am using version 5.1.0. I have had same issue in fewer subjects when I used the older version as well. Any comments about that?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all
Hi Ayaz
what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2)
cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote:
Dear All,
After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV.
Any suggestions? I need to calculate normalized volumes.
Regards
Ayaz
The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
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.
The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
Hi all,
Using previous versions of FreeSurfer, we have used the eTIV as a covariate for our volumetric analyses. We have been using the eTIV numbers from 5.1.0 for new studies. What would you recommend using for subjects who have been run with 5.1.0? Can you make the template available publicly, or would it be legitimate to take the eTIV from 5.0 and the aparc stats from 5.1.0?
Thanks, ~Sue
* * ** *** ***** ******** ************* Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher@bu.edu * * ** *** ***** ******** *************
On Jul 16, 2012, at 4:17 PM, Bruce Fischl wrote:
can you send us an example? In the ones we've looked at the older versions were more stable. Alternatively, we can send you a new template that Avi Snyder generated that you could try out
cheers Bruce
On Mon, 16 Jul 2012, Ayaz, Muhammad wrote:
Well, I am using version 5.1.0. I have had same issue in fewer subjects when I used the older version as well. Any comments about that?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all
Hi Ayaz
what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2)
cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote:
Dear All,
After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV.
Any suggestions? I need to calculate normalized volumes.
Regards
Ayaz
The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
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.
The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Sue
you could take the eTIV from 5.0 and the aparc stats from 5.1.0. I believe we already distribute the updated template but it's not used. Nick: do you want to send around a patch to recon-all that people can use before 5.2 comes out?
thanks Bruce
On Tue, 17 Jul 2012, Susan Ruiz wrote:
Hi all, Using previous versions of FreeSurfer, we have used the eTIV as a covariate for our volumetric analyses. We have been using the eTIV numbers from 5.1.0 for new studies. What would you recommend using for subjects who have been run with 5.1.0? Can you make the template available publicly, or would it be legitimate to take the eTIV from 5.0 and the aparc stats from 5.1.0?
Thanks, ~Sue
Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher@bu.edu
On Jul 16, 2012, at 4:17 PM, Bruce Fischl wrote:
can you send us an example? In the ones we've looked at the older versions were more stable. Alternatively, we can send you a new template that Avi Snyder generated that you could try out cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Well, I am using version 5.1.0. I have had same issue in fewer subjects when I used the older version as well. Any comments about that? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all Hi Ayaz what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2) cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. 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. The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Bruce, Nick, Muhammad et al.,
I noticed that there is an updated mri_segstats for download in the release notes on the wiki, but that appears to be for the SupraTentorial Volume rather than the eTIV. If the patch is available, that would be greatly appreciated (and preferable to running everyone through 5.0). Muhammad--thanks for your question about this since we had not noticed!
Thanks all, ~Sue
* * ** *** ***** ******** ************* Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher@bu.edu * * ** *** ***** ******** *************
On Jul 17, 2012, at 9:50 AM, Bruce Fischl wrote:
Hi Sue
you could take the eTIV from 5.0 and the aparc stats from 5.1.0. I believe we already distribute the updated template but it's not used. Nick: do you want to send around a patch to recon-all that people can use before 5.2 comes out?
thanks Bruce
On Tue, 17 Jul 2012, Susan Ruiz wrote:
Hi all, Using previous versions of FreeSurfer, we have used the eTIV as a covariate for our volumetric analyses. We have been using the eTIV numbers from 5.1.0 for new studies. What would you recommend using for subjects who have been run with 5.1.0? Can you make the template available publicly, or would it be legitimate to take the eTIV from 5.0 and the aparc stats from 5.1.0? Thanks, ~Sue
Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher@bu.edu
On Jul 16, 2012, at 4:17 PM, Bruce Fischl wrote:
can you send us an example? In the ones we've looked at the older versions were more stable. Alternatively, we can send you a new template that Avi Snyder generated that you could try out cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Well, I am using version 5.1.0. I have had same issue in fewer subjects when I used the older version as well. Any comments about that? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all Hi Ayaz what version are you running? There appears to be an instability in the eTIV calculation in just version 5.1 (not before or in the upcoming 5.2) cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. 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. The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Sue, mri_segstats does not compute the eTIV itself, it just gets it from the transform matrix. doug
On 07/18/2012 09:33 AM, Susan Ruiz wrote:
Hi Bruce, Nick, Muhammad et al.,
I noticed that there is an updated mri_segstats for download in the release notes on the wiki, but that appears to be for the SupraTentorial Volume rather than the eTIV. If the patch is available, that would be greatly appreciated (and preferable to running everyone through 5.0). Muhammad--thanks for your question about this since we had not noticed!
Thanks all, ~Sue
Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher@bu.edu mailto:smosher@bu.edu
On Jul 17, 2012, at 9:50 AM, Bruce Fischl wrote:
Hi Sue
you could take the eTIV from 5.0 and the aparc stats from 5.1.0. I believe we already distribute the updated template but it's not used. Nick: do you want to send around a patch to recon-all that people can use before 5.2 comes out?
thanks Bruce
On Tue, 17 Jul 2012, Susan Ruiz wrote:
Hi all, Using previous versions of FreeSurfer, we have used the eTIV as a covariate for our volumetric analyses. We have been using the eTIV numbers from 5.1.0 for new studies. What would you recommend using for subjects who have been run with 5.1.0? Can you make the template available publicly, or would it be legitimate to take the eTIV from 5.0 and the aparc stats from 5.1.0? Thanks, ~Sue
Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smosher@bu.edu mailto:smosher@bu.edu
On Jul 16, 2012, at 4:17 PM, Bruce Fischl wrote:
can you send us an example? In the ones we've looked at theolder versions were more stable. Alternatively, we can send you a new template that Avi Snyder generated that you could try out
cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Well, I am using version 5.1.0. I have had same issue infewer subjects when I used the older version as well. Any comments about that?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 16, 2012 3:04 PM To: Ayaz, Muhammad Cc: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] sum of WM and GM coming out tobe bigger than ICV after recon-all
Hi Ayaz what version are you running? There appears to be aninstability in the
eTIV calculation in just version 5.1 (not before or inthe upcoming 5.2)
cheers Bruce On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: Dear All, After running recon-all, I noticed several subjectsthat sum of WM and GM is
bigger than ICV. I have re-run these subjects andthe results is the same
sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalizedvolumes.
Regards Ayaz The information contained in this message and anyattachments is intended
only for the use of the individual or entity towhich it is addressed, and
may contain information that is PRIVILEGED,CONFIDENTIAL, and exempt from
disclosure under applicable law. If you are not theintended recipient, you
are prohibited from copying, distributing, or usingthe information. Please
contact the sender immediately by return e-mail anddelete the original
message from your system. The information in this e-mail is intended only for theperson to whom it is
addressed. If you believe this e-mail was sent to you inerror and the e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contactthe sender and properly
dispose of the e-mail. The information contained in this message and anyattachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.
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The information in this e-mail is intended only for the personto 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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Ayaz, Muhammad -
Bruce Fischl -
Douglas N Greve -
Susan Ruiz