Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres?
Thank you Sabrina
see if this tool is what you need. It allows you to map to the homolgous vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres?
Thank you Sabrina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html You mentioned editing pctsurfcon to set white matter and gray matter in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity ratio
see if this tool is what you need. It allows you to map to the homolgous vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ 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.
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html You mentioned editing pctsurfcon to set white matter and gray matter in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity ratio
see if this tool is what you need. It allows you to map to the homolgous vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Absolutely, sorry for the confusion. I am looking at decreased ipsilesional myelination signal intensity in patients with unilateral strokes. The goal is to run the T1 scans through FreeSurfer, then determine the ratio of signal intensity - contralesional: ipsilesional.
Thanks, Sabrina
On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html You mentioned editing pctsurfcon to set white matter and gray matter in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity ratio
see if this tool is what you need. It allows you to map to the homolgous vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
on a voxel-by-voxel basis or averaged over an ROI?
On 12/04/2015 12:56 PM, Sabrina Yu wrote:
Absolutely, sorry for the confusion. I am looking at decreased ipsilesional myelination signal intensity in patients with unilateral strokes. The goal is to run the T1 scans through FreeSurfer, then determine the ratio of signal intensity - contralesional: ipsilesional.
Thanks, Sabrina
On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for
both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
You mentioned editing pctsurfcon to set white matter and gray matter
in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu
Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity ratio
see if this tool is what you need. It allows you to map to the homolgous vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think averaged over an ROI is what is best. Any way to do this in FreeSurfer?
Thanks, Sabrina
On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
on a voxel-by-voxel basis or averaged over an ROI?
On 12/04/2015 12:56 PM, Sabrina Yu wrote:
Absolutely, sorry for the confusion. I am looking at decreased ipsilesional myelination signal intensity in patients with unilateral strokes. The goal is to run the T1 scans through FreeSurfer, then determine the ratio of signal intensity - contralesional: ipsilesional.
Thanks, Sabrina
On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for
both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
You mentioned editing pctsurfcon to set white matter and gray matter
in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu
Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity ratio
see if this tool is what you need. It allows you to map to the homolgous vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
there should be a {lh,rh}.w-g.pct.stats files in $SUBJECTS_DIR/subject/stats. That will have the mean gray-white contrast for each ROI in the aparc. Does that work for you?
On 12/04/2015 01:29 PM, Sabrina Yu wrote:
I think averaged over an ROI is what is best. Any way to do this in FreeSurfer?
Thanks, Sabrina
On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
on a voxel-by-voxel basis or averaged over an ROI?
On 12/04/2015 12:56 PM, Sabrina Yu wrote:
Absolutely, sorry for the confusion. I am looking at decreased ipsilesional myelination signal intensity in patients with unilateral strokes. The goal is to run the T1 scans through FreeSurfer, then determine the ratio of signal intensity - contralesional: ipsilesional.
Thanks, Sabrina
On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for
both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
You mentioned editing pctsurfcon to set white matter and gray matter
in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu
Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity ratio
see if this tool is what you need. It allows you to map to the
homolgous
vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of
white
matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug, those are calculated by pctsurfcon correct?
Is there also a way to separately measure white matter intensity, not a gray-white contrast?
Thanks
On Fri, Dec 4, 2015 at 10:38 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
there should be a {lh,rh}.w-g.pct.stats files in $SUBJECTS_DIR/subject/stats. That will have the mean gray-white contrast for each ROI in the aparc. Does that work for you?
On 12/04/2015 01:29 PM, Sabrina Yu wrote:
I think averaged over an ROI is what is best. Any way to do this in FreeSurfer?
Thanks, Sabrina
On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
on a voxel-by-voxel basis or averaged over an ROI?
On 12/04/2015 12:56 PM, Sabrina Yu wrote:
Absolutely, sorry for the confusion. I am looking at decreased ipsilesional myelination signal intensity in patients with unilateral strokes. The goal is to run the T1 scans through FreeSurfer, then determine the ratio of signal intensity - contralesional: ipsilesional.
Thanks, Sabrina
On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for
both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
You mentioned editing pctsurfcon to set white matter and gray matter
in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu
Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity ratio
see if this tool is what you need. It allows you to map to the
homolgous
vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of
white
matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi again,
Just following up with my last email. Also, is it more accurate to compare the gray-white contrast on both hemispheres in the same ROI than to compare white matter intensity only?
Thanks, Sabrina
On Fri, Dec 4, 2015 at 10:53 AM -0800, "Sabrina Yu" <sabrina.yu2@ucalgary.camailto:sabrina.yu2@ucalgary.ca> wrote:
Thanks Doug, those are calculated by pctsurfcon correct?
Is there also a way to separately measure white matter intensity, not a gray-white contrast?
Thanks
On Fri, Dec 4, 2015 at 10:38 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
there should be a {lh,rh}.w-g.pct.stats files in $SUBJECTS_DIR/subject/stats. That will have the mean gray-white contrast for each ROI in the aparc. Does that work for you?
On 12/04/2015 01:29 PM, Sabrina Yu wrote:
I think averaged over an ROI is what is best. Any way to do this in FreeSurfer?
Thanks, Sabrina
On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
on a voxel-by-voxel basis or averaged over an ROI?
On 12/04/2015 12:56 PM, Sabrina Yu wrote:
Absolutely, sorry for the confusion. I am looking at decreased ipsilesional myelination signal intensity in patients with unilateral strokes. The goal is to run the T1 scans through FreeSurfer, then determine the ratio of signal intensity - contralesional: ipsilesional.
Thanks, Sabrina
On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for
both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
You mentioned editing pctsurfcon to set white matter and gray matter
in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu
Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity ratio
see if this tool is what you need. It allows you to map to the
homolgous
vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of
white
matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 12/04/2015 01:53 PM, Sabrina Yu wrote:
Thanks Doug, those are calculated by pctsurfcon correct?
yes
Is there also a way to separately measure white matter intensity, not a gray-white contrast?
You can re-run pctsurfcon specifying the tmp dir. When you do this it will not delete the tmp dir. That dir will have wm and gm separately. You can then run mri_segstats (see the command line in pctsurfcon)
Thanks
On Fri, Dec 4, 2015 at 10:38 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
there should be a {lh,rh}.w-g.pct.stats files in $SUBJECTS_DIR/subject/stats. That will have the mean gray-white contrast for each ROI in the aparc. Does that work for you?
On 12/04/2015 01:29 PM, Sabrina Yu wrote:
I think averaged over an ROI is what is best. Any way to do this in FreeSurfer?
Thanks, Sabrina
On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
on a voxel-by-voxel basis or averaged over an ROI?
On 12/04/2015 12:56 PM, Sabrina Yu wrote:
Absolutely, sorry for the confusion. I am looking at decreased ipsilesional myelination signal intensity in patients with unilateral strokes. The goal is to run the T1 scans through FreeSurfer, then determine the ratio of signal intensity - contralesional:
ipsilesional.
Thanks, Sabrina
On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I guess I'm not sure what you are trying to do. Can you elaborate?
On 12/3/15 6:24 PM, Sabrina Yu wrote:
Hi Doug,
Thanks for the quick reply. Is Xhemi only for measuring volumes for
both hemispheres?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
You mentioned editing pctsurfcon to set white matter and gray matter
in this email thread here. Can this be used to measure of white matter intensity for lh only, and then rh only? This email thread sounded promising for what I need, but am also unsure of how to input set wm and gm commands.
Thanks, Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu
Sent: Thursday, December 3, 2015 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Left and right white matter intensity
ratio
see if this tool is what you need. It allows you to map to the
homolgous
vertex on the contralateral hemisphere http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 12/03/2015 05:25 PM, Sabrina Yu wrote:
Hi there,
Would it be possible to use pctsurfcon to calculate the ratio of
white
matter signal intensity between left and right hemispheres?
Thank you Sabrina
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Sabrina Yu