**CIGAL Reference Manual, Chapter 1 (Topics): background running**
===== Running CIGAL for background recording =====

To start CIGAL in background mode, you should got to the folder where you have your **CIGAL_Physio** shortcut (see [[jvs:cigal:manual:chapter1:background_config_cigal|Configuring CIGAL for background recording]]).

Double-click the **CIGAL_Physio** shortcut to launch CIGAL in background mode. 

The only command you are likely to need will be in the "Physio" menu at the top of the CIGAL window.\\
It has 3 options:\\
  * Show behavior - this will let you see all the physiological (and eye-position if you have it on) signals simultaneously. You can choose to see the live real-time signals or to redisplay previously recorded data. You should check the real-time display at least once before you start recording (and preferably also between runs during the session) to make sure that the physiological transducers are working properly. See **Physio troubleshooting** below if you don't see signals you expect to see.
  * Record physiological signals (or something like that) - this will start a CIGAL real-time paradigm that just records the physiological data. It is set up to run for 15 minutes, but you will be able to stop it as soon as your task ends (see below). When you are ready to start CIGAL in the background (i.e. __after__ the MRTech has "prepped" the scanner), enter '**w**' to have CIGAL start and wait for the scanner trigger.
  * Reconfigure display - this option allows you to change your CIGAL display configuration.  You probably won't need this very often.

To record data:\\
  * select Physio -> Record physiological signals
  * wait until the Tech has prepped the scanner
  * press 'w' at the prompt, to wait for the scanner
  * switch to your other program's window and start your task and the scanner as normal
  * when the task is done, go back to CIGAL's window and enter
    * <Control>E -- this will cause CIGAL to end its recording
  * in the data saving window, enter the scanner's __Exam number__ and the scanner's __series number__ for the scan you just finished (ask the Tech if you are not sure). You can ignore all the other fields in the save data window.

CIGAL will put all the data it records in one session in a folder named with the __Exam number__ you entered in the  saving data dialog. You will see separate text files for each channel of recorded data for each scan series. Each text file has 2 columns of numbers: time (in secs) and the analog signal value. Time=0 is the time that the first MR image was acquired (make sure your __disdaq__ and __TR__ settings in CIGAL match your scan protocol settings (see those parameters in menu: Settings -> Scan settings).

The other important output file is a "pdigm" file for each scan series recorded. The "pdigm" data file contains a copy of all your CIGAL settings, and all of the data recorded during each run. For a graphical view of your physio data you can display the data contents of a "pdigm" file using:\\
  * Physio -> Show behavior -> Saved pdigm file

**See Also:**\\

[[jvs:cigal:manual:chapter1:background|Overview of compatibility for running CIGAL in background]]\\
[[jvs:cigal:manual:chapter1:background_config_cigal|Configuring CIGAL for background recording]]\\
[[jvs:cigal:manual:chapter1:background_config_eprime|Configuring EPrime for compatibility with CIGAL in background]]\\
[[jvs:cigal:manual:chapter1:background_config_presentation|Configuring Presentation for compatibility with CIGAL in background]]\\
[[jvs:cigal:manual:chapter1:background_config_matlab|Configuring Matlab for compatibility with CIGAL in background]]\\
[[jvs:cigal:manual:chapter1:background_start|Starting CIGAL for physio recording in the background]]

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