Brain Imaging & Analysis Center

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== Running ttests ==

To see the activation maps on fScan, open the appropriate functional file (or if one has been created, the aligned.wdf file). Once this file has been opened on fScan, make sure that the file accurately corresponds to the run-time log. Look at the first few slices of the functional file. If these are considerably brighter than the later slices, the disdaqs were not properly removed from the file and the appropriate delay will have to be calculated to account for this. If the first few slices do not differ from the later slices, then the disdaqs were properly accounted for and there is no need to make an additional delay when running the behavioral file. 

//Run-time reference command// 

See also [[CmdLine]]

To run an image of the functional file based on the behavioral files, open a command line window and enter:
   *-r run1list.txt delay 4.5 -ttest 1 2 

This command has several components. The **-r** is the [[jvs:fscan:manual:chapter2:reference| reference]] command which will run the timing index created in the run1list.txt file (see [[jvs:fscan:manual:chapter1:run_lists|Run Lists]]). The **delay** parameter accounts for the hemodynamic delay in brain imaging from a test beginning to the appropriate brain activation in response. 4.5 seconds is a typical delay value. Note: any issues with disdaqs may qualify as an additional delay.

Finally, [[jvs:fscan:manual:chapter2:ttest|-ttest]] will run a comparison between conditions **1** and **2**, which were the labels used in the run1list file. This means that the activation map will compare all the brain activity in the rest (1) portion of the run to the activity (2) portion. Any activity in the **2** section which does not appear in the **1** section will be shown. When the command has been typed, press enter.

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