Hi Jorge,
The global measurement enters in the model as a nuisance, not as an
effect of interest. Even if the estimator is inconsistent, it is still
useful as such. About which is noisier, it turns out that in general,
the bigger the structure, the less measurement noise is present. From
the structural measurements we use, the global ones are certainly those
with higher SNR, including brain volumes, average cortical thickness and
total area -- even if, e.g. brain volume is based on a single
measurement rather than on some sort of average.
All the best,
Anderson
On 27/03/12 01:50, jorge luis wrote:
I think we must be careful about including noisy large scale
measurements as global nuisance covariates in the General Linear Model
(GLM). The GLM assumes that the independent variables are measured
almost without error (eg. see
http://en.wikipedia.org/wiki/Errors-in-variables_models). For
instance, mean cortical thickness or mean global activity in fMRI (as
the mean of many values) should not be as noisy as Intracranial Volume
estimates (or the estimated volume of any neuroanatomical structure).
-Jorge
------------------------------------------------------------------------
*De:* Anderson Winkler <andersonwink...@hotmail.com>
*Para:* freesurfer@nmr.mgh.harvard.edu
*Enviado:* Lunes 26 de marzo de 2012 13:56
*Asunto:* Re: [Freesurfer] Cortical Normalization Questions
Hi Jeff and all,
For normalization (i.e., divide the measurement under study by
some
global measurement), I would not argue favourably, as this
procedure can
bias the results in the opposite direction if a global effect
is present.
Instead, include it as a covariate is not as harmful. My
suggestion is,
when there is no clear approach about using or not a global
measurement
as a nuisance, the relationships between the measurement under
study,
the independent variable, and the putative nuisance should be
calculated, and models with and without the nuisance should be
analysed
and presented. The discussion should consider both analyses
together,
and enough information should be presented so that the final
interpretation is left to the reader.
Specifically for area, I suggest analysing and presenting two
models:
(1) without any global measurement and (2) with global area as
nuisance.
If brain volume (whichever way it is measured) is to be
considered a
potential nuisance for the disorder you are analysing, it can be
included in the model #2 above, even given that they are not
orthogonal
to each other, and are related to global area. Non-orthogonality
between the nuisance variables is not a problem as it is when
effects of
interest are involved.
Hope this helps!
All the best,
Anderson
On 23/03/12 11:29, Michael Harms wrote:
> Our reply to that is here
> http://bjp.rcpsych.org/content/196/5/414.2.long
>
> which reminded me of other papers that have also used a
global thickness
> measure to covary for mean cortical thickness and thereby
"address whether
> any regional thickness differences were in excess of global
cortical
> thickness differences between groups" -- see references
[1,4] in our
> Reply.
>
> cheers,
> -MH
>
>> Hi Michael and others,
>>
>> maybe it's this one:
>>
>> http://bjp.rcpsych.org/content/196/5/414.1.long
>>
>> best,
>> -joost
>>
>>
>> On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms
>> <mha...@conte.wustl.edu <mailto:mha...@conte.wustl.edu>>wrote:
>>
>>> Hi Jeff,
>>> I personally like the idea of using average thickness as a
covariate to
>>> control for a reduction in "whole brain" thickness, and
have used that
>>> approach in a paper. If the Abstract that you mentioned
indicated that
>>> this is flawed, I'd be curious to know what the reason was...
>>>
>>> cheers,
>>> -MH
>>>
>>> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
>>>> Hi Jeff
>>>>
>>>> yes, I think this is still our recommendation for
thickness, although
>>>> perhaps David Salat can verify. As far as surface area,
you might get
>>>> Anderson Winkler to send you a preprint of his newly
accepted paper on
>>>> surface area comparisons and how to do them properly. I
would have
>>> said
>>>> normalize by the 2/3 root of ICV (maybe David can comment
on this as
>>> well)
>>>> cheers
>>>> Bruce
>>>>
>>>>
>>>> On Thu, 22 Mar 2012, Jeff Sadino wrote:
>>>>
>>>>> Hello,
>>>>> For cortical thickness normalizations, Bruce said not to
normalize
>>> based on a HBM
>>>>> abstract
>>>>> (
>>>
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html).
>>> Is
>>>>> this still the consensus?
>>>>>
>>>>> For cortical volume, it is pretty standard to normalize
to eTIV.
>>>>>
>>>>> For cortical surface area (jacobian), I couldn't find any
>>> information
>>> on the wiki.
>>>>> Does anyone have any recommendations?
>>>>>
>>>>> Thank you,
>>>>> Jeff
>>>>>
>>>>>
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