FMRI

Organize the subject's data

Put raw data into:

subjid/date/raw

Hereafter referred to as the session directory Make event files (parfiles) and put the in

subjid/date/Stimuli/parfiles

Initialize an mrVista session

In a MATLAB terminal change to the session directory and open mrInit

mrInit

Add files to mrVista session

Fill in the session description

Open Inplane view

mrVista

And run motion correction

Analysis -> Motion Compensation -> Within + Between Scan

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

GLM -> Assign Parfiles to Scan
GLM -> Grouping -> Group Scans
GLM -> Apply CLM/Contrast New 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.