Hello,
I've read that cortical thickness analyses are limited to the cortex and cannot be used to examine subcortical grey matter. But does "subcortical grey matter" refer to deep gray matter structures such as the hippocampus, the basal ganglia or the nucleus accumbens - all of which are still technically part of the "cerebral cortex" - or does it in fact refer to gray matter nuclei surrounded by white matter, for which it would not be possible to model a white & a pial surface?
Thank you! Francesco
Hi Francesco, This wiki page has pretty good definitions for the morphometry stats. Let us know if you want to clarify anything though.
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
-Louis
On Tue, 25 Mar 2014, Francesco Puccettone wrote:
Hello,
I've read that cortical thickness analyses are limited to the cortex and cannot be used to examine subcortical grey matter. But does "subcortical grey matter" refer to deep gray matter structures such as the hippocampus, the basal ganglia or the nucleus accumbens - all of which are still technically part of the "cerebral cortex" - or does it in fact refer to gray matter nuclei surrounded by white matter, for which it would not be possible to model a white & a pial surface?
Thank you! Francesco
Hi Louis, thanks! I am still not sure whether or not structures such as the hippocampus and the amygdala are considered part of the cortex by freesurfer (they are referred to as `subcortical` but I think an anatomist would say they are in fact part of the cerebral cortex), and whether it makes sense to also calculate thickness for them, or just volume as detailed in the wiki page. --Francesco
On 25 March 2014 18:59, Louis Nicholas Vinke vinke@nmr.mgh.harvard.eduwrote:
Hi Francesco, This wiki page has pretty good definitions for the morphometry stats. Let us know if you want to clarify anything though.
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
-Louis
On Tue, 25 Mar 2014, Francesco Puccettone wrote:
Hello,
I've read that cortical thickness analyses are limited to the cortex and
cannot be used to examine subcortical grey
matter. But does "subcortical grey matter" refer to deep gray matter
structures such as the hippocampus, the basal
ganglia or the nucleus accumbens - all of which are still technically
part of the "cerebral cortex" - or does it in
fact refer to gray matter nuclei surrounded by white matter, for which
it would not be possible to model a white & a
pial surface?
Thank you! Francesco
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Hi Francesco
no, they are not
cheers Bruce
Tue, 25 Mar 2014, Francesco Puccettone wrote:
Hi Louis, thanks! I am still not sure whether or not structures such as the hippocampus and the amygdala are considered part of the cortex by freesurfer (they are referred to as `subcortical` but I think an anatomist would say they are in fact part of the cerebral cortex), and whether it makes sense to also calculate thickness for them, or just volume as detailed in the wiki page. --Francesco
On 25 March 2014 18:59, Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu wrote: Hi Francesco, This wiki page has pretty good definitions for the morphometry stats. Let us know if you want to clarify anything though.
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Tue, 25 Mar 2014, Francesco Puccettone wrote: > Hello, > > I've read that cortical thickness analyses are limited to the cortex and cannot be used to examine subcortical grey > matter. But does "subcortical grey matter" refer to deep gray matter structures such as the hippocampus, the basal > ganglia or the nucleus accumbens - all of which are still technically part of the "cerebral cortex" - or does it in > fact refer to gray matter nuclei surrounded by white matter, for which it would not be possible to model a white & a > pial surface? > > Thank you! > Francesco > >
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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.
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-
Bruce Fischl -
Francesco Puccettone -
Louis Nicholas Vinke