Wallace:fMRI: Difference between revisions
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== Before you Begin == | |||
Before you begin running fMRI studies you'll need to get access to CORES so that you can book time on the scanner. You may be able to be added to an existing project. Work with Walter to set up access with the appropriate people. | |||
== Experiment Design == | == Experiment Design == | ||
Revision as of 07:51, 19 May 2014
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Wallace Lab
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Before you BeginBefore you begin running fMRI studies you'll need to get access to CORES so that you can book time on the scanner. You may be able to be added to an existing project. Work with Walter to set up access with the appropriate people. Experiment DesignTypes of fMRI designThere are 3 main types of scan series that you will use in an fMRI experiment. Rapid Event-RelatedBlock DesignResting StateCreating CodeTo run an fMRI experiment you'll need to write some code that will interface with the scanner and present stimuli in the right order at the right time. For the most part, creating new code will involve taking someone's old code and updating the stimulus array variable. It's a good idea to test things out at the mock scanner in case the scanner software was updated in a way that no longer works well with the code, or if an errant comma or semi-colon found its way into the the code. When creating a stimulus array for a rapid event-related fMRI experiment, you'll need to pseudo-randomize the stimulus order in a way that is compatible for deconvolution analysis. The best way to do this is a program called optseq2. AFNIYou'll need AFNI for MRI analysis. Go to Lab Notebook > Installing software for instructions. Data AnalysisGetting raw data from the scannerAfter a scan you will need to get the data from the scanner to our server. Creating a cortical surface modelIt's easier to view fMRI data on a 3D cortical surface model instead in SUMA of slice by slice in the AFNI. The process takes a while to run (~8) and is best done overnight. To make sure your computer continues to run while you are away, you'll need to configure your energy settings. Go to System Preferences > Energy Saver and click "Prevent computer from sleeping automatically when the display is off". This allow your computer to continue to run even when the screen saver comes on. |
