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Dear Freesurfer Experts,
I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools.
I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3).
I am trying to use LME model with random effects y-int and time from the base line.
Based on the LME tutorial and the questions and answers from Freesurfer support list:
Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ....
To see the difference between group g0 and group g1, I constructed the following contrast matrix using the tutorial provided in LME MATLAB tools
C = [zeros(1,3) [1 0 0] zeros(1,4)]; CM.C=[zeros(1,3) [1 0 0] zeros(1,4)];
Based on the tutorial I run the following functions.
rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere); F_rhstats = lme_mass_F(rhstats,CM); fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig');
nv=length(rhstats); Beta2 = zeros(1,nv); for i=1:nv if ~isempty(rhstats(i).Bhat) Beta2(i) = rhstats(i).Bhat(2); end; end;
rhmri1 = rhmri; rhmri1.volsz(4) = 1; fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh');
[detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0);
fs_write_Y(sided_pval,rhmri1,'spval.mgh');
When I view sig.mgh using tksurfer I see regions with red and blue color.
1) Does the result shows the oveall change for all the five time points? 2) How do I know the difference between the two groups for each 5 time points? 3) Does red means thickness of group A is lgreater than thickness of group B? 4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the information from the file?
With regards
Getaneh
Hi Kersten,
I am sorry I did not make the question more specific.
I have three groups. I want see the power analysis by checking the sample size calculation for the cortical thickness analysis .
[sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr)
my question is how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability) to calculate the sample size of the pairs .
Based on your suggestion to get Dhat and phisqhat I have to run " lme_fit_FS(X,[1,2],y ,ni)"
When I run
lme_fit_FS(X,[1,2],y ,ni), where Y is obtained from the following
[Y,mri] = fs_read_Y('lh.thickness_sm10.mgh'), I get error.
Which function with what argument is good to use to find Dhat and phisqhat?
Are these values the same for left and right cortical thickness data?
I am sorry for the inconvenience .
with regards
Getaneh
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.ha "rvard.edu> on behalf of Diers, Kersten /DZNE Kersten.Diers@dzne.de Sent: Thursday, January 11, 2018 3:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME
Hi,
I am not entirely sure that I understand the goal of this particular analysis, so I don't have any suggestions at the moment.
Maybe you could give some more detail, if this is still an issue.
Best regards,
Kersten
-----Original Message----- From: "Tefera, Getaneh B" Getaneh.B.Tefera@uth.tmc.edu Reply-to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME Date: Wed, 10 Jan 2018 17:58:58 +0100
Dear Kersten,
Thank you so much.
When I run the procedure with left and right cortical thickness data I get different phisqhat values Phisqhat:0.2530 for the left and Phisqhat:0.0903 for the right
The Dhat matrix is also different.
Is that Ok?
If so , shall I consider two sample sizes for the left and right?
With regards
Getaneh
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces @nmr.mgh.harvard.edu] On Behalf Of Diers, Kersten /DZNE Sent: Wednesday, January 10, 2018 7:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME
Hi Getaneh,
the estimates for D and phisq for a given analysis are contained within the data structure that is returned by the lme_fit_FS procedure.
I.e. for the tutorial data, the command was:
total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni);
Dhat and phisqhat are fields of the 'total_hipp_vol_stats' structure, and can be accessed by typing 'total_hipp_vol_stats.Dhat' and 'total_hipp_vol_stats.phisqhat', respectively.
Best regards,
Kersten
-----Original Message----- From: "Tefera, Getaneh B" Getaneh.B.Tefera@uth.tmc.edu Reply-to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME Date: Tue, 9 Jan 2018 23:02:08 +0100
Hi Kersten.
Thank you very much .
I am not planning a new design for sample size calculation.
Can you please help me how to find those values?
Thank you
Getaneh
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mg h.harvard.edu> on behalf of Diers, Kersten /DZNE <Kersten.Diers@dzne.d e
Sent: Tuesday, January 9, 2018 5:56 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME
Hi Getaneh,
please find my responses below.
-----Original Message----- From: "Tefera, Getaneh B" Getaneh.B.Tefera@uth.tmc.edu Reply-to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] LME Date: Mon, 8 Jan 2018 22:54:49 +0100
Dear Freesurfer experts,
I have three groups g0, g1, and g2.
I am trying to use LME model with random effects y-int and time from the base line.
Based on the LME tutorial and the questions and answers from Freesurfer support list:
Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ...
The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1
The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1
1) Is this contrast matrix correct to observe pairwise slope difference?
In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)]
This is a correct matrix, but only for the particular design given in the tutorial, i.e. 4 groups and several covariates. Also, it is not strictly speaking a pairwise test, but will indicate if there is *any* difference between the slopes of the groups (i.e. it will give only one F- and p-value). If you specifically want to test differences between particular pairs, use contrast matrices with just a single row.
2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial?
If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1]
It makes sense to look at the overall effect prior to looking at pairwise differences. If you don't have any additional covariates, that matrix is OK for looking the overall effect. Otherwise, add as many columns of zeros as you have covariates, similar to the tutorial.
3) How can we interpret the result for this contrast matrix?
This is an F-test to detect if there is any difference between the slopes of the groups.
4) How can I obtain B1, B2, ... ?
Consider the following command from the tutorial:
total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni);
Then B1 and B2 will be the first two entries of total_hipp_vol_stats.Bhat
[sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr _pr)
5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)?
If you are planning a new design, these estimates should be based on prior knowledge and can be derived e.g. from a pilot study or from the literature.
Best regards,
Kersten
With regards
Getaneh
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