Hello,
For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations?
Thank you, Jeff
Hi Jeff
yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well)
cheers Bruce
On Thu, 22 Mar 2012, Jeff Sadino wrote:
Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations?
Thank you, Jeff
Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in "whole brain" thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was...
cheers, -MH
On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
Hi Jeff
yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well)
cheers Bruce
On Thu, 22 Mar 2012, Jeff Sadino wrote:
Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations?
Thank you, Jeff
_______________________________________________ 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.
Yes, I think Mike's approach is a good one also, although you have to be clear about the somewhat different hypothesis you are testing
On Mar 22, 2012, at 9:15 PM, Michael Harms mharms@conte.wustl.edu wrote:
Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in "whole brain" thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was...
cheers, -MH
On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
Hi Jeff
yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well)
cheers Bruce
On Thu, 22 Mar 2012, Jeff Sadino wrote:
Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations?
Thank you, Jeff
_______________________________________________ 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 Michael and others,
maybe it's this one:
http://bjp.rcpsych.org/content/196/5/414.1.long
best, -joost
On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mharms@conte.wustl.eduwrote:
Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in "whole brain" thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was...
cheers, -MH
On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
Hi Jeff
yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as
well)
cheers Bruce
On Thu, 22 Mar 2012, Jeff Sadino wrote:
Hello, For cortical thickness normalizations, Bruce said not to normalize
based on a HBM
abstract (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is
this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any information
on the wiki.
Does anyone have any recommendations?
Thank you, Jeff
_______________________________________________ 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
Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long
which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby "address whether any regional thickness differences were in excess of global cortical thickness differences between groups" -- see references [1,4] in our Reply.
cheers, -MH
Hi Michael and others,
maybe it's this one:
http://bjp.rcpsych.org/content/196/5/414.1.long
best, -joost
On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mharms@conte.wustl.eduwrote:
Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in "whole brain" thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was...
cheers, -MH
On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
Hi Jeff
yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have
said
normalize by the 2/3 root of ICV (maybe David can comment on this as
well)
cheers Bruce
On Thu, 22 Mar 2012, Jeff Sadino wrote:
Hello, For cortical thickness normalizations, Bruce said not to normalize
based on a HBM
abstract (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is
this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any
information on the wiki.
Does anyone have any recommendations?
Thank you, Jeff
_______________________________________________ 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
Hi Jeff and all,
For normalization (i.e., divide the measurement under study by some global measurement), I would not argue favourably, as this procedure can bias the results in the opposite direction if a global effect is present.
Instead, include it as a covariate is not as harmful. My suggestion is, when there is no clear approach about using or not a global measurement as a nuisance, the relationships between the measurement under study, the independent variable, and the putative nuisance should be calculated, and models with and without the nuisance should be analysed and presented. The discussion should consider both analyses together, and enough information should be presented so that the final interpretation is left to the reader.
Specifically for area, I suggest analysing and presenting two models: (1) without any global measurement and (2) with global area as nuisance.
If brain volume (whichever way it is measured) is to be considered a potential nuisance for the disorder you are analysing, it can be included in the model #2 above, even given that they are not orthogonal to each other, and are related to global area. Non-orthogonality between the nuisance variables is not a problem as it is when effects of interest are involved.
Hope this helps!
All the best,
Anderson
On 23/03/12 11:29, Michael Harms wrote:
Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long
which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby "address whether any regional thickness differences were in excess of global cortical thickness differences between groups" -- see references [1,4] in our Reply.
cheers, -MH
Hi Michael and others,
maybe it's this one:
http://bjp.rcpsych.org/content/196/5/414.1.long
best, -joost
On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mharms@conte.wustl.eduwrote:
Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in "whole brain" thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was...
cheers, -MH
On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
Hi Jeff
yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have
said
normalize by the 2/3 root of ICV (maybe David can comment on this as
well)
cheers Bruce
On Thu, 22 Mar 2012, Jeff Sadino wrote:
Hello, For cortical thickness normalizations, Bruce said not to normalize
based on a HBM
abstract (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is
this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any
information on the wiki.
Does anyone have any recommendations?
Thank you, Jeff
_______________________________________________ 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
Thank you everyone for your great input. After reading through all of the suggestions and references, I like the idea of using ICV rather than global averages, at least for this current study. However, I do have one more question. All the papers normalize on surface area. If we want to present the Jacobian values, does it make sense to normalize the Jacobian values to the ICV? Or are the Jacobians conceptionally too different from surface areas to do this?
Thank you, Jeff
On Fri, Mar 23, 2012 at 1:29 AM, Michael Harms mharms@conte.wustl.eduwrote:
Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long
which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby "address whether any regional thickness differences were in excess of global cortical thickness differences between groups" -- see references [1,4] in our Reply.
cheers, -MH
Hi Michael and others,
maybe it's this one:
http://bjp.rcpsych.org/content/196/5/414.1.long
best, -joost
On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mharms@conte.wustl.eduwrote:
Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in "whole brain" thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was...
cheers, -MH
On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
Hi Jeff
yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have
said
normalize by the 2/3 root of ICV (maybe David can comment on this as
well)
cheers Bruce
On Thu, 22 Mar 2012, Jeff Sadino wrote:
Hello, For cortical thickness normalizations, Bruce said not to normalize
based on a HBM
abstract (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html).
Is
this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any
information on the wiki.
Does anyone have any recommendations?
Thank you, Jeff
_______________________________________________ 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
Hello,
Thank you Michael for your input. My feeling was that surface area would scale with ICV. In any case, is there any recommendation on how to normalize the Jacobian? My other ramble is that since it is already mapped into a common space, would I normalize the Jacobian, or would I have to normalize its precurser (surface area) measurement and then re-calculate the Jacobian? My last ramble is that since the Jacobian is non-linear, is it possible to normalize it in a simple linear manner, or would it be a more complicated non-linear normalization?
I hope that makes sense. Any feedback would be very greatly helpful! Mahalo, Jeff
Hi Jeff, I'm confused here. ICV and surface area are two very different things.
cheers, -MH
On Thu, Apr 12, 2012 at 12:06 PM, Jeff Sadino jsadino.queens@gmail.comwrote:
Thank you everyone for your great input. After reading through all of the suggestions and references, I like the idea of using ICV rather than global averages, at least for this current study. However, I do have one more question. All the papers normalize on surface area. If we want to present the Jacobian values, does it make sense to normalize the Jacobian values to the ICV? Or are the Jacobians conceptionally too different from surface areas to do this?
Thank you, Jeff
On Fri, Mar 23, 2012 at 1:29 AM, Michael Harms mharms@conte.wustl.eduwrote:
Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long
which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby "address whether any regional thickness differences were in excess of global cortical thickness differences between groups" -- see references [1,4] in our Reply.
cheers, -MH
Hi Michael and others,
maybe it's this one:
http://bjp.rcpsych.org/content/196/5/414.1.long
best, -joost
On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mharms@conte.wustl.eduwrote:
Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in "whole brain" thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was...
cheers, -MH
On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
Hi Jeff
yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper
on
surface area comparisons and how to do them properly. I would have
said
normalize by the 2/3 root of ICV (maybe David can comment on this as
well)
cheers Bruce
On Thu, 22 Mar 2012, Jeff Sadino wrote:
Hello, For cortical thickness normalizations, Bruce said not to normalize
based on a HBM
abstract (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html ).
Is
this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area (jacobian), I couldn't find any
information on the wiki.
Does anyone have any recommendations?
Thank you, Jeff
_______________________________________________ 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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Why do you want the jacobian? The surface area is a more interpretable measure. If you use surface area, make sure you get the patch for mris_preproc. doug
On 4/23/12 8:07 PM, Jeff Sadino wrote:
Hello,
Thank you Michael for your input. My feeling was that surface area would scale with ICV. In any case, is there any recommendation on how to normalize the Jacobian? My other ramble is that since it is already mapped into a common space, would I normalize the Jacobian, or would I have to normalize its precurser (surface area) measurement and then re-calculate the Jacobian? My last ramble is that since the Jacobian is non-linear, is it possible to normalize it in a simple linear manner, or would it be a more complicated non-linear normalization?
I hope that makes sense. Any feedback would be very greatly helpful! Mahalo, Jeff
Hi Jeff, I'm confused here. ICV and surface area are two very different things.
cheers, -MH
On Thu, Apr 12, 2012 at 12:06 PM, Jeff Sadino <jsadino.queens@gmail.com mailto:jsadino.queens@gmail.com> wrote:
Thank you everyone for your great input. After reading through all of the suggestions and references, I like the idea of using ICV rather than global averages, at least for this current study. However, I do have one more question. All the papers normalize on surface area. If we want to present the Jacobian values, does it make sense to normalize the Jacobian values to the ICV? Or are the Jacobians conceptionally too different from surface areas to do this? Thank you, Jeff On Fri, Mar 23, 2012 at 1:29 AM, Michael Harms <mharms@conte.wustl.edu <mailto:mharms@conte.wustl.edu>> wrote: Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby "address whether any regional thickness differences were in excess of global cortical thickness differences between groups" -- see references [1,4] in our Reply. cheers, -MH > Hi Michael and others, > > maybe it's this one: > > http://bjp.rcpsych.org/content/196/5/414.1.long > > best, > -joost > > > On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms > <mharms@conte.wustl.edu <mailto:mharms@conte.wustl.edu>>wrote: > >> >> Hi Jeff, >> I personally like the idea of using average thickness as a covariate to >> control for a reduction in "whole brain" thickness, and have used that >> approach in a paper. If the Abstract that you mentioned indicated that >> this is flawed, I'd be curious to know what the reason was... >> >> cheers, >> -MH >> >> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: >> > Hi Jeff >> > >> > yes, I think this is still our recommendation for thickness, although >> > perhaps David Salat can verify. As far as surface area, you might get >> > Anderson Winkler to send you a preprint of his newly accepted paper on >> > surface area comparisons and how to do them properly. I would have >> said >> > normalize by the 2/3 root of ICV (maybe David can comment on this as >> well) >> > >> > cheers >> > Bruce >> > >> > >> > On Thu, 22 Mar 2012, Jeff Sadino wrote: >> > >> > > Hello, >> > > For cortical thickness normalizations, Bruce said not to normalize >> based on a HBM >> > > abstract >> > > ( >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). >> Is >> > > this still the consensus? >> > > >> > > For cortical volume, it is pretty standard to normalize to eTIV. >> > > >> > > For cortical surface area (jacobian), I couldn't find any >> information >> on the wiki. >> > > Does anyone have any recommendations? >> > > >> > > Thank you, >> > > Jeff >> > > >> > > >> > _______________________________________________ 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 >> >
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