Hi Alejandra, I don't work with children, so I'll let someone else (Lilla? Rudolph?) answer. doug ps. Please remember to copy the list on responses. Thanks!
On 05/08/2013 01:19 AM, Alejandra Infante wrote:
Thank you! I might have asked this at the training, but I am still not clear on whether the estimated ICV (from freesurfer) is reliable if your population of interest are children? Or would you recommend manual edits (when needed) after checking the quality of the talairach registration file using tkregister2 --s subjid --fstal --surfs?
On Tue, May 7, 2013 at 7:52 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV and/or Buckner et al. (2004) NeuroImage <https://surfer.nmr.mgh.harvard.edu/fswiki/NeuroImage> 23:724-738. "Basically, total intracranial volume is found to correlate with the determinant of the transform matrix used to align an image with an atlas. The work demonstrates that a one-parameter scaling factor provides a reasonable TIV estimation. This method uses an atlas based spatial normalization procedure, and requires that the *talairach.xfm* is correct. " This performs the talairach registration for a subject. Then, based only on the numbers in the matrix, it estimates the ICV based on subjects that had similar matrices. doug On 5/7/13 9:42 PM, Alejandra Infante wrote:Hi, I understand that ICV is an estimated measure based on a standard talairach transformation; however, I want to know how freesurfer is defining intracranial volume (i.e., is this a representation of everything within the cranium as the name implies or is it an estimate of total brain volume, which would not include space between skull and dura)?. We are using fs vesion 5.1 -- M. Alejandra Infante Doctoral Student SDSU/UCSD Joint Doctoral Program in Clinical Psychology Phone: (858) 449-2950 <tel:%28858%29%20449-2950> E-Mail: infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.-- M. Alejandra Infante Doctoral Student SDSU/UCSD Joint Doctoral Program in Clinical Psychology Phone: (858) 449-2950 E-Mail: infante.alejandra.m@gmail.com mailto:infante.alejandra.m@gmail.com
Thank you!
Sent from my iPhone
On May 8, 2013, at 8:17 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Alejandra, I don't work with children, so I'll let someone else (Lilla? Rudolph?) answer. doug ps. Please remember to copy the list on responses. Thanks!
On 05/08/2013 01:19 AM, Alejandra Infante wrote:
Thank you! I might have asked this at the training, but I am still not clear on whether the estimated ICV (from freesurfer) is reliable if your population of interest are children? Or would you recommend manual edits (when needed) after checking the quality of the talairach registration file using tkregister2 --s subjid --fstal --surfs?
On Tue, May 7, 2013 at 7:52 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV and/or Buckner et al. (2004) NeuroImage https://surfer.nmr.mgh.harvard.edu/fswiki/NeuroImage 23:724-738.
"Basically, total intracranial volume is found to correlate with the determinant of the transform matrix used to align an image with an atlas. The work demonstrates that a one-parameter scaling factor provides a reasonable TIV estimation. This method uses an atlas based spatial normalization procedure, and requires that the *talairach.xfm* is correct. "
This performs the talairach registration for a subject. Then, based only on the numbers in the matrix, it estimates the ICV based on subjects that had similar matrices.
doug
On 5/7/13 9:42 PM, Alejandra Infante wrote:
Hi, I understand that ICV is an estimated measure based on a standard talairach transformation; however, I want to know how freesurfer is defining intracranial volume (i.e., is this a representation of everything within the cranium as the name implies or is it an estimate of total brain volume, which would not include space between skull and dura)?. We are using fs vesion 5.1
-- M. Alejandra Infante Doctoral Student SDSU/UCSD Joint Doctoral Program in Clinical Psychology Phone: (858) 449-2950 tel:%28858%29%20449-2950 E-Mail: infante.alejandra.m@gmail.com mailto:infante.alejandra.m@gmail.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
-- M. Alejandra Infante Doctoral Student SDSU/UCSD Joint Doctoral Program in Clinical Psychology Phone: (858) 449-2950 E-Mail: infante.alejandra.m@gmail.com mailto:infante.alejandra.m@gmail.com
-- 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/
Hi,
A follow up question pertaining to this issue for me is how good is the measure of the ICV when dealing with subjects having prior resections or significant atrophy. I am using FreeSurfer v5.1.
Thank you M. Goryawala Post-Doctoral Associate Florida International University Miami, FL
On Wed, May 8, 2013 at 11:53 AM, Alejandra Infante < infante.alejandra.m@gmail.com> wrote:
Thank you!
Sent from my iPhone
On May 8, 2013, at 8:17 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Alejandra, I don't work with children, so I'll let someone else
(Lilla? Rudolph?) answer.
doug ps. Please remember to copy the list on responses. Thanks!
On 05/08/2013 01:19 AM, Alejandra Infante wrote:
Thank you! I might have asked this at the training, but I am still not
clear on whether the estimated ICV (from freesurfer) is reliable if your population of interest are children? Or would you recommend manual edits (when needed) after checking the quality of the talairach registration file using tkregister2 --s subjid --fstal --surfs?
On Tue, May 7, 2013 at 7:52 PM, Douglas Greve <
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV and/or Buckner et al. (2004) NeuroImage https://surfer.nmr.mgh.harvard.edu/fswiki/NeuroImage 23:724-738.
"Basically, total intracranial volume is found to correlate with the determinant of the transform matrix used to align an image with an atlas. The work demonstrates that a one-parameter scaling factor provides a reasonable TIV estimation. This method uses an atlas based spatial normalization procedure, and requires that the *talairach.xfm* is correct. "
This performs the talairach registration for a subject. Then, based only on the numbers in the matrix, it estimates the ICV based on subjects that had similar matrices.
doug
On 5/7/13 9:42 PM, Alejandra Infante wrote:
Hi, I understand that ICV is an estimated measure based on a standard talairach transformation; however, I want to know how freesurfer is defining intracranial volume (i.e., is this a representation of everything within the cranium as the name implies or is it an estimate of total brain volume, which would not include space between skull and dura)?. We are using fs vesion 5.1
-- M. Alejandra Infante Doctoral Student SDSU/UCSD Joint Doctoral Program in Clinical Psychology Phone: (858) 449-2950 tel:%28858%29%20449-2950 E-Mail: infante.alejandra.m@gmail.com mailto:infante.alejandra.m@gmail.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:
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.
-- M. Alejandra Infante Doctoral Student SDSU/UCSD Joint Doctoral Program in Clinical Psychology Phone: (858) 449-2950 E-Mail: infante.alejandra.m@gmail.com <mailto:
infante.alejandra.m@gmail.com>
-- 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
I don't know, I don't think the test has ever been done. It probably depends upon how good the talairach registration is. doug
On 05/08/2013 03:12 PM, Mohammed Goryawala wrote:
Hi,
A follow up question pertaining to this issue for me is how good is the measure of the ICV when dealing with subjects having prior resections or significant atrophy. I am using FreeSurfer v5.1.
Thank you M. Goryawala Post-Doctoral Associate Florida International University Miami, FL
On Wed, May 8, 2013 at 11:53 AM, Alejandra Infante <infante.alejandra.m@gmail.com mailto:infante.alejandra.m@gmail.com> wrote:
Thank you! Sent from my iPhone On May 8, 2013, at 8:17 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Alejandra, I don't work with children, so I'll let someone else (Lilla? Rudolph?) answer. > doug > ps. Please remember to copy the list on responses. Thanks! > > On 05/08/2013 01:19 AM, Alejandra Infante wrote: >> Thank you! I might have asked this at the training, but I am still not clear on whether the estimated ICV (from freesurfer) is reliable if your population of interest are children? Or would you recommend manual edits (when needed) after checking the quality of the talairach registration file using tkregister2 --s subjid --fstal --surfs? >> >> >> On Tue, May 7, 2013 at 7:52 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> >> It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV >> and/or Buckner et al. (2004) NeuroImage >> <https://surfer.nmr.mgh.harvard.edu/fswiki/NeuroImage> 23:724-738. >> >> "Basically, total intracranial volume is found to correlate with >> the determinant of the transform matrix used to align an image >> with an atlas. The work demonstrates that a one-parameter scaling >> factor provides a reasonable TIV estimation. This method uses an >> atlas based spatial normalization procedure, and requires that the >> *talairach.xfm* is correct. " >> >> This performs the talairach registration for a subject. Then, >> based only on the numbers in the matrix, it estimates the ICV >> based on subjects that had similar matrices. >> >> doug >> >> >> >> On 5/7/13 9:42 PM, Alejandra Infante wrote: >>> Hi, >>> I understand that ICV is an estimated measure based on a standard >>> talairach transformation; however, I want to know how freesurfer >>> is defining intracranial volume (i.e., is this a representation >>> of everything within the cranium as the name implies or is it an >>> estimate of total brain volume, which would not include space >>> between skull and dura)?. We are using fs vesion 5.1 >>> >>> >>> -- M. Alejandra Infante >>> Doctoral Student >>> SDSU/UCSD Joint Doctoral Program in Clinical Psychology >>> Phone: (858) 449-2950 <tel:%28858%29%20449-2950> <tel:%28858%29%20449-2950> >>> E-Mail: infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com> >>> <mailto:infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. >> >> >> >> >> -- >> M. Alejandra Infante >> Doctoral Student >> SDSU/UCSD Joint Doctoral Program in Clinical Psychology >> Phone: (858) 449-2950 <tel:%28858%29%20449-2950> >> E-Mail: infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com> <mailto:infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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 <mailto: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
to add to this, the registration it uses is performed on the whole head, so skull/skin/dura/fat/neck is included, which make the registration less susceptible to mis-registration due to lesions/atrophy/resection.
n.
On Wed, 2013-05-08 at 15:15 -0400, Douglas N Greve wrote:
I don't know, I don't think the test has ever been done. It probably depends upon how good the talairach registration is. doug
On 05/08/2013 03:12 PM, Mohammed Goryawala wrote:
Hi,
A follow up question pertaining to this issue for me is how good is the measure of the ICV when dealing with subjects having prior resections or significant atrophy. I am using FreeSurfer v5.1.
Thank you M. Goryawala Post-Doctoral Associate Florida International University Miami, FL
On Wed, May 8, 2013 at 11:53 AM, Alejandra Infante <infante.alejandra.m@gmail.com mailto:infante.alejandra.m@gmail.com> wrote:
Thank you! Sent from my iPhone On May 8, 2013, at 8:17 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Alejandra, I don't work with children, so I'll let someone else (Lilla? Rudolph?) answer. > doug > ps. Please remember to copy the list on responses. Thanks! > > On 05/08/2013 01:19 AM, Alejandra Infante wrote: >> Thank you! I might have asked this at the training, but I am still not clear on whether the estimated ICV (from freesurfer) is reliable if your population of interest are children? Or would you recommend manual edits (when needed) after checking the quality of the talairach registration file using tkregister2 --s subjid --fstal --surfs? >> >> >> On Tue, May 7, 2013 at 7:52 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> >> It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV >> and/or Buckner et al. (2004) NeuroImage >> <https://surfer.nmr.mgh.harvard.edu/fswiki/NeuroImage> 23:724-738. >> >> "Basically, total intracranial volume is found to correlate with >> the determinant of the transform matrix used to align an image >> with an atlas. The work demonstrates that a one-parameter scaling >> factor provides a reasonable TIV estimation. This method uses an >> atlas based spatial normalization procedure, and requires that the >> *talairach.xfm* is correct. " >> >> This performs the talairach registration for a subject. Then, >> based only on the numbers in the matrix, it estimates the ICV >> based on subjects that had similar matrices. >> >> doug >> >> >> >> On 5/7/13 9:42 PM, Alejandra Infante wrote: >>> Hi, >>> I understand that ICV is an estimated measure based on a standard >>> talairach transformation; however, I want to know how freesurfer >>> is defining intracranial volume (i.e., is this a representation >>> of everything within the cranium as the name implies or is it an >>> estimate of total brain volume, which would not include space >>> between skull and dura)?. We are using fs vesion 5.1 >>> >>> >>> -- M. Alejandra Infante >>> Doctoral Student >>> SDSU/UCSD Joint Doctoral Program in Clinical Psychology >>> Phone: (858) 449-2950 <tel:%28858%29%20449-2950> <tel:%28858%29%20449-2950> >>> E-Mail: infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com> >>> <mailto:infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. >> >> >> >> >> -- >> M. Alejandra Infante >> Doctoral Student >> SDSU/UCSD Joint Doctoral Program in Clinical Psychology >> Phone: (858) 449-2950 <tel:%28858%29%20449-2950> >> E-Mail: infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com> <mailto:infante.alejandra.m@gmail.com <mailto:infante.alejandra.m@gmail.com>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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 <mailto: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
-
Alejandra Infante -
Douglas N Greve -
Mohammed Goryawala -
Nick Schmansky