Re: [Freesurfer] mean cortical thickness not equal to averaged ROIs cortical thickness

[Nabin Koirala]

Thank you.

Regards,
Nabin

On Sat, Jun 25, 2016 at 5:36 PM, Bruce Fischl 
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 > >
>> 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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Re: [Freesurfer] mean cortical thickness not equal to averaged ROIs cortical thickness

[Bruce Fischl]

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 
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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Re: [Freesurfer] mean cortical thickness not equal to averaged ROIs cortical thickness

[Nabin Koirala]

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 
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
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] mean cortical thickness not equal to averaged ROIs cortical thickness

[Bruce Fischl]

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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