On 12/15/2021 8:36 AM, Laura Willers de Souza wrote:
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Dear Douglas,
Again, thanks for the reply.
Please check if I understand correctly:
* First I do the contrast [0 0 -1 1] to test if there is an
interaction between diagnosis and cortisol; if there is, I do DOSS
[1 -1 0], if there isnt’t, I continue with DODS.
* Having no interaction, I do the contrast [1 -1 0 0] to check if
only the diagnosis changes cortical thickness regardless of cortisol.
Did I interpret correctly?
You have it backwards. If there is no interaction, use DOSS. If there
is an interaction, consult a statistician. Fortunately, there is no
interaction (whew!)
And how do I check if cortisol changes cortical thickness regardless
of diagnosis (assuming there is no interaction)?
[0 0 1] with DOSS
Thanks again!
Best,
*Laura Willers de Souza*
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
---------------------------------------------------------------------------------------------------
*De:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Enviado:* terça-feira, 14 de dezembro de 2021
*Para:* Laura Willers de Souza <laura.w.deso...@hotmail.com>
*Cc:*freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Assunto:* Re: [Freesurfer] Questions about contrasts
This contrast will do it: [1 -1 0 0]
But I would first test [0 0 -1 1] to see if the slopes are different.
If not, then use [1 -1 0] with DOSS instead of DODS
---------------------------------------------------------------------------------------------------
*De:* Laura Willers de Souza <laura.w.deso...@hotmail.com>
*Enviado:* terça-feira, 14 de dezembro de 2021 17:30
*Para:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Cc:*freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Assunto:* Re: Questions about contrasts
Dear Douglas,
Thank you so much for your answer!
Sorry, but I don't think I explained myself correctly in the previous
email.
I want to analyze the difference in cortical thickness between two
groups (CU and CI), adjusting for a covariate (cortisol CSF) and the
interaction between them.
So my model would be: cortical thickness ~ diagnosis + CSF cortisol +
diagnosis*CSF cortisol
Using the GLM DODS, the contrasts, according to the wiki example
(https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V
<https://secure-web.cisco.com/1qbucUNWhNS-2uW6Lox1w2bMK8EUHU0lm2XC7ywMcgAz1opgFdJ9TpOloRtF1uTmyVc70aldT5QkaELBu9kC0X6YiGpVUzZ3hV6ImEDrYAPF9VgAmDOudc6SysPVlhaUvzzGFirVYNLChsA_roK3faZNzYnWbdGPEJSgasor3qtQpKeAN7XvnQ4X24hWQfi35Rh8kF9yIsndHzOZGNxOdCH7U2CUMc9KxEL3N9u2-8weS-Fz01NHj2B_xMyBA8BlbS0n_wekioRXCPViGU3a_0zVQxE5Wu9sLPwFsQ3peECtbgAqHVmzWbyks9AhB3fWY/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdf2G1V>),
would be:
* To verify if only the diagnosis regression coefficient is
significant (diagnosis changes cortical thickness regardless of
cortisol):
1 -1 0 0
* To verify if the regression coefficient of the interaction between
diagnosis and cortisol is significant (the two change cortical
thickness dependently):
0 0 1 -1
* To verify if only the cortisol regression coefficient is
significant (cortisol changes cortical thickness regardless of
diagnosis):
0 0 0.5 0.5
Are these contrasts corret to represent the model we designed?
Thank you so much again!
Best regards,
*Laura Willers de Souza*
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
---------------------------------------------------------------------------------------------------
*De:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Enviado:* terça-feira, 12 de dezembro de 2021 18:23
*Para:* Laura Willers de Souza <laura.w.deso...@hotmail.com>
*Cc:*freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Assunto:* Re: [Freesurfer] Questions about contrasts
The model is actually, two independent linear models:
thicknessCU = CUOffset + CUcortisol*CUslope
thicknessCI = CIOffset + CIcortisol*CIslope
There will be four regression parameters:
[CUOffset CUslope CIOffset CIslope]
---------------------------------------------------------------------------------------------------
*De:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Enviado:* terça-feira, 12 de dezembro de 2021 10:48
*Para:* Laura Willers de Souza <laura.w.deso...@hotmail.com>
*Cc:*freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Assunto:* Re: [Freesurfer] Questions about contrasts
Hello FreeSurfer Developers,
I want to perform an analysis of the difference between two groups
incortical thickness, having cortisol levels as covariate.
This is my model: cortical thickness ~ pathology (CU/CI) +
CSFcortisol + pathology*CSF cortisol
From the GLM DODS analysis I want to know if:
* the regression coefficient is significant only for the difference
between groups,
this could possibly mean two things: the difference in offset [1 -1 0
0]or the difference in slopes ([0 0 1 -1]
* or only for cortisol,
[0 0 0.5 0.5] will test whether the cortisol slope is different than 0
* or for both,
both what?
* or if the coefficient of the intercept between group and cortisol
is significant.
this does not make sense to me
Is my FSGD file (attached) correct? What would the contrasts look
like?
---------------------------------------------------------------------------------------------------
*De:* Laura Willers de Souza <laura.w.deso...@hotmail.com>
*Enviado:* terça-feira, 09 de dezembro de 2021 19:50
*Para:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Cc:*freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Assunto:* Questions about contrasts
Hello FreeSurfer Developers,
I want to perform an analysis of the difference between two groups in
cortical thickness, having cortisol levels as covariate.
This is my model: cortical thickness ~ pathology (CU/CI) + CSF
cortisol + pathology*CSF cortisol
From the GLM DODS analysis I want to know if:
* the regression coefficient is significant only for the difference
between groups,
* or only for cortisol,
* or for both,
* or if the coefficient of the intercept between group and cortisol
is significant.
Is my FSGD file (attached) correct? What would the contrasts look like?
Thanks in advance!
*Laura Willers de Souza *
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
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