Hi freesurfer team,
I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the mean cortical thickness obtained by aparcstats2table. I would expect it to be the same or very close but I checked it for more than 100 subjects and they are significantly different. Am I missing something silly here ?
Thank you.
Regards, Nabin
Hi Nabin
unless the areas are the same size, the mean of the areal means won't equal the overall mean.
cheers Bruce On Sat, 25 Jun 2016, Nabin Koirala wrote:
Hi freesurfer team, I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the mean cortical thickness obtained by aparcstats2table. I would expect it to be the same or very close but I checked it for more than 100 subjects and they are significantly different. Am I missing something silly here ?
Thank you.
Regards, Nabin
Dear Bruce,
Thank you for the response. So, I more thing if I want to get the mean cortical thickness for whole brain I could simply take the mean between both hemisphere ? If I understood right from the FAQ.
Q. I am trying to measure the global mean cortical thickness (i.e combined across hemispheres), how would I do this?
A: One suggestion is to use the surface area of each hemisphere as the weighting factor. In which case the global mean thickness including both hemispheres would be given by:
bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea)
If you use the values in the ?h.aparc.stats, it already factors out the 'unknown' region, so you don't have to do it yourself.
Regards,
Nabin
On Sat, Jun 25, 2016 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Nabin
unless the areas are the same size, the mean of the areal means won't equal the overall mean.
cheers Bruce
On Sat, 25 Jun 2016, Nabin Koirala wrote:
Hi freesurfer team,
I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the mean cortical thickness obtained by aparcstats2table. I would expect it to be the same or very close but I checked it for more than 100 subjects and they are significantly different. Am I missing something silly here ?
Thank you.
Regards, Nabin
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the mean across both lh.cortex.label and rh.cortex.label should be pretty close. If you want it to be exact you should weight by area then normalize On Sat, 25 Jun 2016, Nabin Koirala wrote:
Dear Bruce, Thank you for the response. So, I more thing if I want to get the mean cortical thickness for whole brain I could simply take the mean between both hemisphere ? If I understood right from the FAQ.
Q. I am trying to measure the global mean cortical thickness (i.e combined across hemispheres), how would I do this?
A: One suggestion is to use the surface area of each hemisphere as the weighting factor. In which case the global mean thickness including both hemispheres would be given by:
bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea)
If you use the values in the ?h.aparc.stats, it already factors out the 'unknown' region, so you don't have to do it yourself.
Regards,
Nabin
On Sat, Jun 25, 2016 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nabin
unless the areas are the same size, the mean of the areal means won't equal the overall mean. cheers Bruce On Sat, 25 Jun 2016, Nabin Koirala wrote: Hi freesurfer team, I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the mean cortical thickness obtained by aparcstats2table. I would expect it to be the same or very close but I checked it for more than 100 subjects and they are significantly different. Am I missing something silly here ? Thank you. Regards, Nabin
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.
Thank you.
Regards, Nabin
On Sat, Jun 25, 2016 at 5:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
the mean across both lh.cortex.label and rh.cortex.label should be pretty close. If you want it to be exact you should weight by area then normalize
On Sat, 25 Jun 2016, Nabin Koirala wrote:
Dear Bruce,
Thank you for the response. So, I more thing if I want to get the mean cortical thickness for whole brain I could simply take the mean between both hemisphere ? If I understood right from the FAQ.
Q. I am trying to measure the global mean cortical thickness (i.e combined across hemispheres), how would I do this?
A: One suggestion is to use the surface area of each hemisphere as the weighting factor. In which case the global mean thickness including both hemispheres would be given by:
bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea)
If you use the values in the ?h.aparc.stats, it already factors out the 'unknown' region, so you don't have to do it yourself.
Regards,
Nabin
On Sat, Jun 25, 2016 at 3:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Nabin
unless the areas are the same size, the mean of the areal means won't equal the overall mean. cheers Bruce On Sat, 25 Jun 2016, Nabin Koirala wrote: Hi freesurfer team, I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the mean cortical thickness obtained by aparcstats2table. I would expect it to be the same or very close but I checked it for more than 100 subjects and they are significantly different. Am I missing something silly here ? Thank you. Regards, Nabin
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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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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.
Dear FreeSurfer experts,
I would like to look at longitudinal thickness data and want to control for total gray matter volume. Should I use that information from the CROSS before anything has been registered and smoothed or from the LONG after they have been registered to the BASE? Also I was wondering if it is useful to control for total gray matter volume when looking at surface area?
Thanks for your help! Clara
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Clara Kühn -
Nabin Koirala