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Both options are correct, although I prefer not modelling baseline so beta reflect change directly detail here https://www.frontiersin.org/articles/10.3389/fnins.2014.00001/full Frontiers | Misconceptions in the use of the General Linear Model applied to functional MRI: a tutorial for junior neuro-imagers | Neuroscience - Frontiers | Peer Reviewed Articles - Open Access Journals<https://www.frontiersin.org/articles/10.3389/fnins.2014.00001/full> www.frontiersin.org Brain Research Imaging Centre, Imaging Sciences, University of Edinburgh, Edinburgh, UK This tutorial presents several misconceptions related to the use the General Linear Model (GLM) in functional Magnetic Resonance Imaging (fMRI). The goal is not to present mathematical proofs but to educate using ... note if you have a single run, no need to do 1 0, you con in this case eqaul you beta cyril ________________________________ From: SPM (Statistical Parametric Mapping) <[log in to unmask]> on behalf of Miguel Ángel Rivas Fernández <[log in to unmask]> Sent: 14 February 2019 08:08 To: [log in to unmask] Subject: [SPM] First level analysis: Contrast in design matrix Dear all, I am doing the first level analysis in a fMRI event-related design using a memory task with two conditions. I performed a t-test in order to compare both conditions but I would like to know how is the brain activation within each condition excluding the variance explained by other conditions and also by movement (including the rp_.txt files as regressors in the model). Could I include in the design matrix the fixation cross like a "baseline condition"? Which of the following options would be correct? OPTION 1. With Fixation: Three conditions in design matrix: Condition A, B, Fixation Condition A > Condition B design matrix: 1 -1 0 Condition B > Condition A design matrix: -1 1 0 Condition A > Fixation design matrix: 1 0 -1 Condition B > Fixation design matrix: 0 1 -1 OPTION 2. Without Fixation: Two conditions in the design matrix: Condition A, B Condition A > Condition B design matrix: 1 -1 Condition B > Condition A design matrix: -1 1 Condition A design matrix: 1 0 Condition B design matrix: 0 1 Any help would be very appreciated. Thanks in advance Best regards, Miguel Ángel Rivas Fernández The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.