Hi Amirhossein, - If you have two time points for all participants, - and the time difference is the same for all you can simply subtract the thickness (or volume) values per participant and run a regular GLM. LME is a little overkill here.
In LME, you have one column of ones, and one of the time (which is 0 and t alternating ) , this is not the time difference! The first time point is at time 0 and the second at time t (in hours or days whatever). If the time really does not matter, you can also put 0 and 1. You can run the model with no random effect or with one random effect. The wiki https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels describes how to compare those models, also how to compute significance. You probably have more columns (also if you do the GLM) e.g. the amount of drug that was given, or who got the drug and who got placebo. Otherwise you cannot check for a drug effect. That column would be the one you are interested in. Without a placebo group, you will find difference across time, but you will not know if they are from the drug or from the fact that people are familiar with the scanner (less head motion) or more annoyed by the scanner (more head motion) or more tired, or more dehydrated, or rehydrated if you give the drug with water, or simply a time-of-the-day effect, or scanner heats up etc. Some of these confounders are problematic anyway, as the drug can have a sedative effect (less motion?) or was given with water (re-hydration). The second can be controlled by giving placebo with the same amount of water. Disentangling motion from drug effect (due to the possible correlation) would only be possible if you separately measure motion or take fMRI or diffusion motion estimates as a proxy for motion during T1. Head motion reduces grey matter estimates: <https://doi.org/10.1016/j.neuroimage.2014.12.006> doi.org<https://doi.org/10.1016/j.neuroimage.2014.12.006> [X]<https://doi.org/10.1016/j.neuroimage.2014.12.006> Dehydration effects: <http://www.ajnr.org/content/36/12/2277.long> [12.cover-source.jpg] Responses of the Human Brain to Mild Dehydration and Rehydration Explored In Vivo by 1H-MR Imaging and Spectroscopy<http://www.ajnr.org/content/36/12/2277.long> ajnr.org<http://www.ajnr.org/content/36/12/2277.long> Best, Martin On 30. Jan 2023, at 15:18, amirhossein manzouri <a.h.manzo...@gmail.com> wrote: Hi, I have 2 sessions of data acquired in the same day for each participant before and after the drug intake. I wonder how to analyse this with LME tool. I create design matrix X in 2 columns, first all ones and second the time differences(which are the same) and wonder if I need to only run the model with one random effect like lhTh0_1RF = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3); And what would be the next steps to get the stats and sig.mgh Best regards, Amirhossein Manzouri
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