document version 1.1

last updated 04 August31 December, 20032

VCortex: Cortex for Windows

(beta version 1.1)

User’s Manual

Laboratory of Neuropsychology, NIMH

TABLE OF CONTENTS

TABLE OF CONTENTS............................................................................................................................................................... 2

1. Introduction...................................................................................................................................................................... 6

1.1. Cortex: A Program for COmputerized Real Time EXperiments...................................................... 6

1.2 Getting the latest version of Cortex............................................................................................................ 7

1.3 Technical Support...................................................................................................................................................... 7

1.4. History (you may skip this part)...................................................................................................................... 7

2. Hardware and Software Requirements.......................................................................................................... 9

2.1 Two-computer Cortex (\VCWin32\VCSend.exe)............................................................................................ 9

2.2 Single-computer Cortex without graphics (\VCWin32\VCSingle.EXE)................................. 11

3. Installation.................................................................................................................................................................... 12

3.1 Data Acquisition Board Setup......................................................................................................................... 12

3.1.1 Typical Keithley/Metrabyte DASH-16 settings................................................................................................. 12

3.1.2 Typical PIO24 or CIO-DIO24 settings................................................................................................................. 12

3.1.3 Typical Computerboard CIO AD-16, CIO-DAS16/F, and CIO-DAS1602/12 settings............................... 12

3.2 Graphics Board Setup............................................................................................................................................. 13

3.3 Data Acquisition Interface Setup................................................................................................................. 13

3.3.1 Spike Flip Flop Circuitry...................................................................................................................................... 13

3.3.2 Thalamus.................................................................................................................................................................... 13

3.3.3 Screw Terminal Interface Diagram for the DASH-16 type boards.................................................................. 14

3.4 Sound Card Setup...................................................................................................................................................... 14

3.5 Serial Connection Setup....................................................................................................................................... 14

3.6 Cortex Software Setup and Program Execution................................................................................ 15

3.6.1 Minimum Files Necessary to run Windows VCortex.......................................................................................... 15

3.6.2 Installing VCSend.exe and VCSingle.exe on the send computer (Win95/98)...................................... 15

3.6.3 Installing the DirectX Receive Program on the receive computer (Win95/98/2000/XP)................... 22

3.7 Touchscreen Setup................................................................................................................................................... 27

3.7.1 Hardware Setup........................................................................................................................................................ 28

3.7.2 Microtouch Touchware Setup............................................................................................................................... 28

3.7.3 Cortex Configuration File Setup for Touchscreen Operation......................................................................... 34

3.8 Uninstalling Cortex............................................................................................................................................... 34

4. Using Cortex..................................................................................................................................................................... 37

4.1. Setting up the experimental conditions.................................................................................................. 37

4.2. Item files........................................................................................................................................................................ 37

4.3. Conditions files......................................................................................................................................................... 39

4.4. Timing files................................................................................................................................................................... 40

4.5. Using the ITEMS, CONDITIONS, and TIMING files in a study................................................................ 41

4.5.1 Deciding on your Experimental Design............................................................................................................... 41

4.6. Customizing Cortex with the Cortex.cfg configuration file.................................................... 42

5. Running VCortex............................................................................................................................................................ 43

5.1 The Main Menu Structure.................................................................................................................................... 43

5.1.1 The File Menu.......................................................................................................................................................... 43

5.1.2 The Edit Menu........................................................................................................................................................... 44

5.1.3 The Options Menu.................................................................................................................................................... 45

5.1.4 The Tools Menu........................................................................................................................................................ 46

5.1.5 The Run Menu........................................................................................................................................................... 47

5.1.6 The Clear Menu....................................................................................................................................................... 47

5.1.7 The View Menu......................................................................................................................................................... 48

5.1.8 The Window Menu................................................................................................................................................... 48

5.1.9 The Help Menu.......................................................................................................................................................... 48

5.2 The File Menu Dialog Boxes................................................................................................................................. 49

5.2.1 File->Load->Item File............................................................................................................................................ 49

5.2.2 File->Load->Condition File................................................................................................................................. 49

5.2.3 File-> Load ->Timing File..................................................................................................................................... 50

5.2.4 File-> Load ->Saved File....................................................................................................................................... 51

5.2.5 File-> Load ->LUT File.......................................................................................................................................... 51

5.2.6 File->Load->External Variables File................................................................................................................. 52

5.2.7 File->Load->Blocks File....................................................................................................................................... 53

5.2.8 File->Save->Item File............................................................................................................................................. 53

5.2.9 File->Save->Condition File.................................................................................................................................. 54

5.2.10 File->Save->Saved File....................................................................................................................................... 54

5.2.11 File->Save->LUT File.......................................................................................................................................... 54

5.2.12 File->Save->External Variables File................................................................................................................ 55

5.2.13 File->Save->Blocks File...................................................................................................................................... 56

5.3 The Edit Menu Dialog Boxes................................................................................................................................ 56

5.3.1 Edit->Individual Item.............................................................................................................................................. 56

5.3.2 Edit->Individual Condition................................................................................................................................... 71

5.3.3 Edit->Timing File->Modify................................................................................................................................... 72

5.3.4 Edit->Timing File->Delete.................................................................................................................................... 73

5.3.5 Edit->External Variables->Generic Externs...................................................................................................... 74

5.3.6 Edit->External Variables->Named Subsets....................................................................................................... 75

5.3.7 Edit->Fixspot Item................................................................................................................................................... 77

5.3.8 Edit->Reference Item............................................................................................................................................... 77

5.3.9 Edit->LUT.................................................................................................................................................................. 78

5.3.10 Edit->Add an Item................................................................................................................................................. 79

5.4 The Options Menu Dialog Boxes........................................................................................................................ 79

5.4.1 Options->Block / Repeat->Sizing........................................................................................................................ 79

5.4.2 Options->Block / Repeat->MasterBlock............................................................................................................ 80

5.4.3 Options->Block/Repeat->Individual Blocks..................................................................................................... 81

5.4.4 Options->General Parameters.............................................................................................................................. 85

5.5 The Tools Menu Dialog Boxes............................................................................................................................ 88

5.5.1 Tools->LUT->Set Number of Palettes.................................................................................................................. 88

5.5.2 Tools->LUT->Activate............................................................................................................................................ 88

5.5.3 Tools->Play->Alone................................................................................................................................................ 89

5.5.4 Tools->Play->With Conditions.......................................................................................................................... 106

5.6 The Run Menu Dialog Boxes............................................................................................................................... 107

5.6.1 Run->Start.............................................................................................................................................................. 107

5.6.2 Run->Resume.......................................................................................................................................................... 109

5.6.3 Run->Stop............................................................................................................................................................... 109

5.7 The Clear Menu Dialog Boxes.......................................................................................................................... 109

5.7.1 Clear->External Variables->All........................................................................................................................ 109

5.7.2 Clear->Blocking->CONDstats........................................................................................................................... 109

5.7.3 Clear->Blocking->BLOCKstats......................................................................................................................... 109

5.7.4 Clear->Blocking->Reset All............................................................................................................................... 109

5.7.5 Clear->Histogram/Rasters................................................................................................................................... 109

5.8 The View Menu Dialog Boxes............................................................................................................................. 109

5.8.1 View->Results of most recent trial->Codes...................................................................................................... 109

5.8.2 View->Results of most recent trial->EOG values............................................................................................ 110

5.8.3 View->Results of most recent trial->EPP values............................................................................................. 111

5.8.4 View->Results of most recent trial->Touch screen values............................................................................. 112

5.8.3 View->Display an Item......................................................................................................................................... 113

5.8.4 View->Display a Condition................................................................................................................................. 113

5.8.5 View->Status Bar................................................................................................................................................... 114

5.9 Window Menu Dialog Boxes............................................................................................................................. 114

5.10 Quick Start Instructions................................................................................................................................ 114

5.10.1 Dual Computer Cortex version (VCSend)...................................................................................................... 114

5.10.2 VCSingle version................................................................................................................................................. 115

6. Limitations of Cortex due to structure and hardware................................................................ 116

6.1. Data storage........................................................................................................................................................... 116

6.2. Data file format................................................................................................................................................... 116

6.3. Interrupt structure............................................................................................................................................ 116

7. Image File Formats and Color Lookup Tables....................................................................................... 117

7.1. Image File Formats............................................................................................................................................... 117

7.1.1 The Cortex Image File Format........................................................................................................................... 117

7.1.2 Image File Formats Available with DirectX version of Cortex.................................................................... 117

7.1.4 Transparency with DirectX receive program................................................................................................... 118

7.2 Movie File Formats................................................................................................................................................. 118

7.2.1 Cortex Movie File Format.................................................................................................................................... 118

7.2.2 Movie File Formats Available with DirectX version of Cortex.....................................................................