Hi everybody,
I have a small problem with an old version of freesurfer. I am studing some data that someone analyzed some months ago using the old version of freesurfer. I am looking for the mean cortical thickness of each hemisphere, but I have found only the thickness af each single area of the segmented cortex in a txt file in the label directory. Can anybody please tell me where I can find the information about the average cortical thickness of each hemisphere? Should I recalculate it averaging all the cortical labeled areas (each weighted on the extention of its surface)?
thank you,
-stefano
do you mean the mean across the entire cortex? If so, mris_anatomical_stats will give you that. On Mon, 10 Jul 2006, Stefano Pellegrini wrote:
Hi everybody,
I have a small problem with an old version of freesurfer. I am studing some data that someone analyzed some months ago using the old version of freesurfer. I am looking for the mean cortical thickness of each hemisphere, but I have found only the thickness af each single area of the segmented cortex in a txt file in the label directory. Can anybody please tell me where I can find the information about the average cortical thickness of each hemisphere? Should I recalculate it averaging all the cortical labeled areas (each weighted on the extention of its surface)?
thank you,
-stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bruce: is this an average weighted on the surface of the cortices or just a pure arithmetic mean? Thanks, Francesca
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 10, 2006 1:50 PM To: Pellegrini, Stefano (NIH/NINDS) [F] Cc: freesurfer Subject: Re: [Freesurfer] old_freesurfer question
do you mean the mean across the entire cortex? If so, mris_anatomical_stats will give you that. On Mon, 10 Jul 2006, Stefano Pellegrini wrote:
Hi everybody,
I have a small problem with an old version of freesurfer. I am studing
some data that someone analyzed some months ago using the old version of freesurfer. I am looking for the mean cortical thickness of each
hemisphere,
but I have found only the thickness af each single area of the
segmented
cortex in a txt file in the label directory. Can anybody please tell
me where
I can find the information about the average cortical thickness of
each
hemisphere? Should I recalculate it averaging all the cortical labeled
areas
(each weighted on the extention of its surface)?
thank you,
-stefano _______________________________________________ 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
not sure I understand what you mean. It is the mean across the surface. As such it will be corrupted by non-cortical regions such as the callosum, although they are only a small % of the surface. If you want to get rid of them you can draw a cortical label and pass it to mris_anatomical_stats with -l <label file>. One of these days I'll get around to writing an automated cortex label, since with the aseg we now have enough info to generate one.
cheers, Bruce
On Mon, 10 Jul 2006, Bagnato, Francesca (NIH/NINDS) [E] wrote:
Bruce: is this an average weighted on the surface of the cortices or just a pure arithmetic mean? Thanks, Francesca
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 10, 2006 1:50 PM To: Pellegrini, Stefano (NIH/NINDS) [F] Cc: freesurfer Subject: Re: [Freesurfer] old_freesurfer question
do you mean the mean across the entire cortex? If so, mris_anatomical_stats will give you that. On Mon, 10 Jul 2006, Stefano Pellegrini wrote:
Hi everybody,
I have a small problem with an old version of freesurfer. I am studing
some data that someone analyzed some months ago using the old version of freesurfer. I am looking for the mean cortical thickness of each
hemisphere,
but I have found only the thickness af each single area of the
segmented
cortex in a txt file in the label directory. Can anybody please tell
me where
I can find the information about the average cortical thickness of
each
hemisphere? Should I recalculate it averaging all the cortical labeled
areas
(each weighted on the extention of its surface)?
thank you,
-stefano _______________________________________________ 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 just mean to ask if such a mean take into account the different surfaces area and correct for that (e.g. geometric mean). Thanks Francesca
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 10, 2006 2:04 PM To: Bagnato, Francesca (NIH/NINDS) [E] Cc: Pellegrini, Stefano (NIH/NINDS) [F]; freesurfer Subject: RE: [Freesurfer] old_freesurfer question
not sure I understand what you mean. It is the mean across the surface. As such it will be corrupted by non-cortical regions such as the callosum, although they are only a small % of the surface. If you want to get rid of them you can draw a cortical label and pass it to mris_anatomical_stats with -l <label file>. One of these days I'll get around to writing an automated cortex label, since with the aseg we now have enough info to generate one.
cheers, Bruce
On Mon, 10 Jul 2006, Bagnato, Francesca (NIH/NINDS) [E] wrote:
Bruce: is this an average weighted on the surface of the cortices or just a pure arithmetic mean? Thanks, Francesca
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 10, 2006 1:50 PM To: Pellegrini, Stefano (NIH/NINDS) [F] Cc: freesurfer Subject: Re: [Freesurfer] old_freesurfer question
do you mean the mean across the entire cortex? If so, mris_anatomical_stats will give you that. On Mon, 10 Jul 2006, Stefano Pellegrini wrote:
Hi everybody,
I have a small problem with an old version of freesurfer. I am studing
some data that someone analyzed some months ago using the old version of freesurfer. I am looking for the mean cortical thickness of each
hemisphere,
but I have found only the thickness af each single area of the
segmented
cortex in a txt file in the label directory. Can anybody please tell
me where
I can find the information about the average cortical thickness of
each
hemisphere? Should I recalculate it averaging all the cortical labeled
areas
(each weighted on the extention of its surface)?
thank you,
-stefano _______________________________________________ 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
actually it's the total gray matter volume (sum of thickness*surface area)
On Mon, 10 Jul 2006, Bagnato, Francesca (NIH/NINDS) [E] wrote:
I just mean to ask if such a mean take into account the different surfaces area and correct for that (e.g. geometric mean). Thanks Francesca
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 10, 2006 2:04 PM To: Bagnato, Francesca (NIH/NINDS) [E] Cc: Pellegrini, Stefano (NIH/NINDS) [F]; freesurfer Subject: RE: [Freesurfer] old_freesurfer question
not sure I understand what you mean. It is the mean across the surface. As such it will be corrupted by non-cortical regions such as the callosum, although they are only a small % of the surface. If you want to get rid of them you can draw a cortical label and pass it to mris_anatomical_stats with -l <label file>. One of these days I'll get around to writing an automated cortex label, since with the aseg we now have enough info to generate one.
cheers, Bruce
On Mon, 10 Jul 2006, Bagnato, Francesca (NIH/NINDS) [E] wrote:
Bruce: is this an average weighted on the surface of the cortices or just a pure arithmetic mean? Thanks, Francesca
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 10, 2006 1:50 PM To: Pellegrini, Stefano (NIH/NINDS) [F] Cc: freesurfer Subject: Re: [Freesurfer] old_freesurfer question
do you mean the mean across the entire cortex? If so, mris_anatomical_stats will give you that. On Mon, 10 Jul 2006, Stefano Pellegrini wrote:
Hi everybody,
I have a small problem with an old version of freesurfer. I am studing
some data that someone analyzed some months ago using the old version of freesurfer. I am looking for the mean cortical thickness of each
hemisphere,
but I have found only the thickness af each single area of the
segmented
cortex in a txt file in the label directory. Can anybody please tell
me where
I can find the information about the average cortical thickness of
each
hemisphere? Should I recalculate it averaging all the cortical labeled
areas
(each weighted on the extention of its surface)?
thank you,
-stefano _______________________________________________ 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
-
Bagnato, Francesca (NIH/NINDS) [E] -
Bruce Fischl -
Stefano Pellegrini