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.tef...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mg h.harvard.edu> on behalf of Diers, Kersten /DZNE <kersten.di...@dzne.de > 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.tef...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harva rd.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1V apJQ8JVoF8oWH1AgfQ&r=f2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=w3Go ND77ORaREflQR6B1sxt8pIPGPzd8Oh_hzfJ_rhk&s=7GFfEuDrrPYWE- NE_mVYzsQUEvfZizwe853OSP2n_Zo&e= The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_co mplianceline&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=f 2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=w3GoND77ORaREflQR6B1sxt8pI PGPzd8Oh_hzfJ_rhk&s=_JumR_-uS8QiP3xZfqqQ73pib0Pi-_MI1tUhsm2z5bA&e= . 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