The contrasts are for DODS, you will need different contrasts for DOSS. I just added something onto that web page for DOSS
On 1/3/2022 10:10 PM, Laura Willers de Souza wrote:
External Email - Use Caution
Hi Douglas,
Actually I have one more question.
I went to look at the contrast examples on the wiki and in the example that fits my analysis (Two Groups (One Factor/Two Levels), One Covariate) it says "DODS only", and you mentioned in the previous email that my analysis turned out to be DOSS, because the interaction is non-significant.
So my question is why on the wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V https://secure-web.cisco.com/1URi9Q-jl56ZpEMHrCqZrpvsv5PT3SKRjQnDVbwQuE-opRgESmFu0WTNlYDWtajuIHMT_w6hWtyhfqdiez9QCELg4ffzmYOtrgQ_wxNcUHZqFwWj4cwqvoAJdCnVN46emE4HMp9FMzZS3OreIqXSlYnBTS3uTaTX-zODfDN2SNvIESLamQSlLhVCJXV3vGAFqpPmaTRVwZoDpcannldUrH6pXKZ8t6xQM_BekqhMg__0dlG_rI7XHFgFFKj_jHml1fBDIxcUbP6L60CZx_bK1SKcsMw9DrJzTzEd9-u8jfQnTLOAcWWK_EXkQxHAFFZWb/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdf2G1V) it's like "DODS only"? My fear is that I have not explained my analysis correctly to you.
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 dgreve@mgh.harvard.edu *Enviado:* domingo, 02 de janeiro de 2022 *Para:* Laura Willers de Souza laura.w.desouza@hotmail.com *Cc:*freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Assunto:* Re: [Freesurfer] Questions about contrasts
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 thereis an interaction, consult a statistician. Fortunately, there is nointeraction (whew!)
And how do I check if cortisol changes cortical thickness regardlessof diagnosis (assuming there is no interaction)?[0 0 1] with DOSS
Thanks again! Best, *Laura Willers de Souza*
*De:* Laura Willers de Souza laura.w.desouza@hotmail.com *Enviado:* quarta-feira, 15 de dezembro de 2021 *Para:* Douglas N. Greve dgreve@mgh.harvard.edu *Cc:*freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Assunto:* Re: Questions about contrasts
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?
And how do I check if cortisol changes cortical thickness regardless of diagnosis (assuming there is no interaction)?
Thanks again!
Best, Laura Willers de Souza
*De:* Douglas N. Greve dgreve@mgh.harvard.edu *Enviado:* terça-feira, 14 de dezembro de 2021 *Para:* Laura Willers de Souza laura.w.desouza@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.desouza@hotmail.com *Enviado:* terça-feira, 14 de dezembro de 2021 17:30 *Para:* Douglas N. Greve dgreve@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 dgreve@mgh.harvard.edu *Enviado:* terça-feira, 12 de dezembro de 2021 18:23 *Para:* Laura Willers de Souza laura.w.desouza@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 dgreve@mgh.harvard.edu *Enviado:* terça-feira, 12 de dezembro de 2021 10:48 *Para:* Laura Willers de Souza laura.w.desouza@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.desouza@hotmail.com *Enviado:* terça-feira, 09 de dezembro de 2021 19:50 *Para:* Douglas N. Greve dgreve@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