[Freesurfer] average cortical thickness measure?

2015-12-17 Thread Maria Kharitonova 
Hi, in response to the average thickness measure (see below). In
?h.aparc.stats, I see a variable ThickAvg, is that it? And then to get the
average thickness across the *entire* cortex, I average across the couple
of dozen regions that it provides?

Thanks!
Maria

>
>
>Message: 7
>Date: Fri, 11 Dec 2015 13:49:23 -0500
>From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] average cortical thickness measure?
>To: freesurfer@nmr.mgh.harvard.edu
>Message-ID: <566b1ab3.9090...@nmr.mgh.harvard.edu>
>Content-Type: text/plain; charset=windows-1252; format=flowed
>
>In ?h.aparc.stats, you'll find a line like
>
># Measure Cortex, MeanThickness, Mean Thickness, 2.40617, mm
>
>You'll have to get the value for each hemi and compute the mean
>
>
>On 12/11/2015 01:38 PM, Maria Kharitonova wrote:
>> I know that the aseg atlas provides a number of voume measures
>> (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a
>> variable for an average cortical thickness? I?d like to see if
>> thickness in some of the regions is associated with a variable of
>> interest over and above an overall main effect, so would like to
>> control for the average thickness, but can?t figure out a good way to
>> do that.
>>
>> Thanks!
>> Maria
>>
>> ?
>> Maria Kharitonova, PhD
>> Research Assistant Professor
>> Department of Medical Social Sciences
>> Northwestern University Feinberg School of Medicine
>> 625 N. Michigan Ave, Suite 2700
>> Chicago, IL 60611
>> Phone: (312) 503-6503
>> Email: maria.khariton...@northwestern.edu
>> <mailto:maria.khariton...@northwestern.edu>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
>--


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Re: [Freesurfer] average cortical thickness measure?

2015-12-17 Thread Bruce Fischl 
Hi Maria

to get the overall average you would need to weight each area by how big it 
is. Probably easier to use mris_anatomical_stats -l lh.cortex.label

cheers
Bruce


cheers
Bruce

On Thu, 17 
Dec 2015, Maria Kharitonova wrote:

> Hi, in response to the average thickness measure (see below). In
> ?h.aparc.stats, I see a variable ThickAvg, is that it? And then to get the
> average thickness across the *entire* cortex, I average across the couple
> of dozen regions that it provides?
>
> Thanks!
> Maria
>
>>
>>
>> Message: 7
>> Date: Fri, 11 Dec 2015 13:49:23 -0500
>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] average cortical thickness measure?
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID: <566b1ab3.9090...@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>> In ?h.aparc.stats, you'll find a line like
>>
>> # Measure Cortex, MeanThickness, Mean Thickness, 2.40617, mm
>>
>> You'll have to get the value for each hemi and compute the mean
>>
>>
>> On 12/11/2015 01:38 PM, Maria Kharitonova wrote:
>>> I know that the aseg atlas provides a number of voume measures
>>> (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a
>>> variable for an average cortical thickness? I?d like to see if
>>> thickness in some of the regions is associated with a variable of
>>> interest over and above an overall main effect, so would like to
>>> control for the average thickness, but can?t figure out a good way to
>>> do that.
>>>
>>> Thanks!
>>> Maria
>>>
>>> ?
>>> Maria Kharitonova, PhD
>>> Research Assistant Professor
>>> Department of Medical Social Sciences
>>> Northwestern University Feinberg School of Medicine
>>> 625 N. Michigan Ave, Suite 2700
>>> Chicago, IL 60611
>>> Phone: (312) 503-6503
>>> Email: maria.khariton...@northwestern.edu
>>> <mailto:maria.khariton...@northwestern.edu>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>>
>>
>> --
>
>
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>
>
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[Freesurfer] average cortical thickness measure?

2015-12-11 Thread Maria Kharitonova 
I know that the aseg atlas provides a number of voume measures (e.g. 
EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a variable for an 
average cortical thickness? I'd like to see if thickness in some of the regions 
is associated with a variable of interest over and above an overall main 
effect, so would like to control for the average thickness, but can't figure 
out a good way to do that.

Thanks!
Maria

-
Maria Kharitonova, PhD
Research Assistant Professor
Department of Medical Social Sciences
Northwestern University Feinberg School of Medicine
625 N. Michigan Ave, Suite 2700
Chicago, IL 60611
Phone: (312) 503-6503
Email: 
maria.khariton...@northwestern.edu

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Re: [Freesurfer] average cortical thickness measure?

2015-12-11 Thread Douglas N Greve 
In ?h.aparc.stats, you'll find a line like

# Measure Cortex, MeanThickness, Mean Thickness, 2.40617, mm

You'll have to get the value for each hemi and compute the mean


On 12/11/2015 01:38 PM, Maria Kharitonova wrote:
> I know that the aseg atlas provides a number of voume measures 
> (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a 
> variable for an average cortical thickness? I’d like to see if 
> thickness in some of the regions is associated with a variable of 
> interest over and above an overall main effect, so would like to 
> control for the average thickness, but can’t figure out a good way to 
> do that.
>
> Thanks!
> Maria
>
> —
> Maria Kharitonova, PhD
> Research Assistant Professor
> Department of Medical Social Sciences
> Northwestern University Feinberg School of Medicine
> 625 N. Michigan Ave, Suite 2700
> Chicago, IL 60611
> Phone: (312) 503-6503
> Email: maria.khariton...@northwestern.edu 
> 
>
>
>
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> Freesurfer mailing list
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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