Yeatman Lab Wiki

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====Organize the subject's data==== Put raw data into: <code>subjid/date/raw</code> Hereafter referred to as the session directory.\\ Make event files (parfiles) and put them in <code>subjid/date/Stimuli/parfiles</code> ====Initialize an mrVista session==== In a MATLAB terminal change to the session directory and open mrInit <code>mrInit</code> Add files to mrVista session\\ {{wiki:mrInit.png?400}}\\ Fill in the session description\\ {{wiki:mrInit_SessionDesc.png?400}} ====Open Inplane view==== <code>mrVista</code> {{wiki:Inplaneview.png?400}} And run motion correction <code>Analysis -> Motion Compensation -> Within + Between Scan</code> ====Fit GLM==== First associate a parfile with each scan and then group all the MotionComp scans so that the GLM is fit to all of them <code>GLM -> Assign Parfiles to Scan GLM -> Grouping -> Group Scans GLM -> Apply CLM/Contrast New Code</code> In the GLM window that comes up set the HRF to SPM Difference of gammas and set the number of TRs (in our case 8) and detrend option to Quadratic.