Hello,
I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)?
Thank you for reply.
Hi Zuzana,
Yes, you can use BrainSegVol as a measurement of brain volume (I'd assume you are using FS <=4.5.0). Note that there is another measurement that you might be interested in, the IntraCranialVol. These measurements tell different things and not necessarily correlate well one with another depending on the sample. BSV considers the voxels labelled as GM and WM, including subcortical structures and cerebellum and so, it correlates better with amount of GM and WM and tends to be more sensitive to pathology, atrophy and aging. ICV is more robust to these effects. You may want to choose the one that is more appropriate to your study.
Also, if you are considering brain volume as a covariate for cortical thickness, it's not necessary. Thickness correlates poorly with brain volume, and these two things are not correlated genetically.
Hope this helps!
All the best,
Anderson
On 24/08/11 05:39, zuzana nedelska wrote:
Hello,
I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)?
Thank you for reply.
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.
A side note: If you are using FS 4.5.0 or earlier, there is also BrainSegVolNotVent, which discount ventricles. If you want to capture effects of aging or atrophy, perhaps this could be more sensitive than BrainSegVol.
On 24/08/11 12:32, Anderson Winkler wrote:
Hi Zuzana,
Yes, you can use BrainSegVol as a measurement of brain volume (I'd assume you are using FS <=4.5.0). Note that there is another measurement that you might be interested in, the IntraCranialVol. These measurements tell different things and not necessarily correlate well one with another depending on the sample. BSV considers the voxels labelled as GM and WM, including subcortical structures and cerebellum and so, it correlates better with amount of GM and WM and tends to be more sensitive to pathology, atrophy and aging. ICV is more robust to these effects. You may want to choose the one that is more appropriate to your study.
Also, if you are considering brain volume as a covariate for cortical thickness, it's not necessary. Thickness correlates poorly with brain volume, and these two things are not correlated genetically.
Hope this helps!
All the best,
Anderson
On 24/08/11 05:39, zuzana nedelska wrote:
Hello,
I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)?
Thank you for reply.
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
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 Anderson:
Your explanation is very well put. I have a question. Suppose one is looking at High Risk datasets (for example Schizophrenia) where the brain morphological alterations are subtle but spread across the brain, which covariate would you use?
thanks,
Alan
[Beth Israel Deaconess Medical Center]
On Wed, Aug 24, 2011 at 12:43 PM, Anderson Winkler < andersonwinkler@hotmail.com> wrote:
** A side note: If you are using FS 4.5.0 or earlier, there is also BrainSegVolNotVent, which discount ventricles. If you want to capture effects of aging or atrophy, perhaps this could be more sensitive than BrainSegVol.
On 24/08/11 12:32, Anderson Winkler wrote:
Hi Zuzana,
Yes, you can use BrainSegVol as a measurement of brain volume (I'd assume you are using FS <=4.5.0). Note that there is another measurement that you might be interested in, the IntraCranialVol. These measurements tell different things and not necessarily correlate well one with another depending on the sample. BSV considers the voxels labelled as GM and WM, including subcortical structures and cerebellum and so, it correlates better with amount of GM and WM and tends to be more sensitive to pathology, atrophy and aging. ICV is more robust to these effects. You may want to choose the one that is more appropriate to your study.
Also, if you are considering brain volume as a covariate for cortical thickness, it's not necessary. Thickness correlates poorly with brain volume, and these two things are not correlated genetically.
Hope this helps!
All the best,
Anderson
On 24/08/11 05:39, zuzana nedelska wrote:
Hello,
I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)?
Thank you for reply.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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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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 Alan,
I'd say it depends on what the study is about, but in principle, I'd think that the covariates should remove what would have potential to be confounding more what the main effect would be. In the example of schizophrenia, I'd choose BrainSegVolNotVent, and run both models, with and without it, and interpret the results combined.
Also, unless if the samples are too small or unless one wants to explicitly test the effect of ICV and/or BV, I don't see any problem in including both ICV and BV in the model, even considering they are well correlated to some extent. The shared variance between them interferes on the beta-estimates for them, but not on the betas for the other regressors that you would be testing, and the part of the variance that is not shared between them will absorb the effects for which they were chosen to be covaryied out.
This is my opinion. Others may think differently.
All the best!
Anderson
On 24/08/11 12:51, Alan Francis wrote:
Hi Anderson: Your explanation is very well put. I have a question. Suppose one is looking at High Risk datasets (for example Schizophrenia) where the brain morphological alterations are subtle but spread across the brain, which covariate would you use? thanks, Alan [Beth Israel Deaconess Medical Center]
On Wed, Aug 24, 2011 at 12:43 PM, Anderson Winkler <andersonwinkler@hotmail.com mailto:andersonwinkler@hotmail.com> wrote:
A side note: If you are using FS 4.5.0 or earlier, there is also BrainSegVolNotVent, which discount ventricles. If you want to capture effects of aging or atrophy, perhaps this could be more sensitive than BrainSegVol. On 24/08/11 12:32, Anderson Winkler wrote:Hi Zuzana, Yes, you can use BrainSegVol as a measurement of brain volume (I'd assume you are using FS <=4.5.0). Note that there is another measurement that you might be interested in, the IntraCranialVol. These measurements tell different things and not necessarily correlate well one with another depending on the sample. BSV considers the voxels labelled as GM and WM, including subcortical structures and cerebellum and so, it correlates better with amount of GM and WM and tends to be more sensitive to pathology, atrophy and aging. ICV is more robust to these effects. You may want to choose the one that is more appropriate to your study. Also, if you are considering brain volume as a covariate for cortical thickness, it's not necessary. Thickness correlates poorly with brain volume, and these two things are not correlated genetically. Hope this helps! All the best, Anderson On 24/08/11 05:39, zuzana nedelska wrote:Hello, I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)? Thank you for reply. _______________________________________________ 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._______________________________________________ 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._______________________________________________ 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.
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.
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