This web page describes how to install and use my ezlog data logging software. This software allows you to measure when different events happened, allowing you to synchronise the timing of different stimuli. Specifically, my software is designed to get a detailed report of when visual/auditory or tactile stimulation occurred relative to brain images. By collecting functional MRI scans that are sensitive to changes in blood flow, we can identify the brain regions that are involved with certain tasks. My software will measure the time when each brain image was acquired as well as logging the time of the stimulus that the participant perceived. This tutorial is broken into four secions:

• Hardware: you need to create a cable that connects your scanner and stimulus presentation computer to a computer that will log the times of stimuli and scans.
• Software: A quick introduction to my ezlog data logging software for Windows.
• Notes: details for using this software effectively.

Hardware You need to create a cable that can connect the different devices that you wish to record. Each device should be able to generate a TTL (transistor-transistor logic) pulse. The diagram on the right illustrates a cable designed to connect the parallel ports of two computers together, as well as connecting to a scanner. This picture shows a coaxial connector plugging into the scanner, matching the TTL output found on Philips Intera scanners with system release 10 or later. Note that the stimulus presentation computer sends outputs through pins 2..5, and these are recorded on the input pins of the data logging computer. In addition, note that the 0volt ground lines (shown in black) connect all devices (on a computer's parallel port, pins 18..25 are all ground lines).

Advanced Hardware

Make sure your scanner is set up to generate pulses with your EPI sequences. For Philips scanners, you go to the 'Dyn' (Dynamic) page of the sequence protocol and set the 'Dyn. Sync. Pulse' to TRUE. Note that this may increase the acquisition time of your volumes (e.g. we recorded the duration of each volume increased by 15ms).

The pulses generated by your scanner should have a duration longer than 1ms. My software only checks the parallel port every millisecond, so it will typically miss very brief pulses. For example, by default the Philips Intera generates a 0.05ms pulse. Furthermore, the input to the parallel port needs to be an electrical TTL pulse (not the optical pulse generated by modern Siemens scanners). Therefore, you may need to build extra hardware to connect your scanner to a PC (regardless of whether the PC is running my software or something else such as EPrime). Below are two very inexpensive circuits I have built myself (they were designed by my dad, Bob Rorden, Phil Moore suggested using the inexpensive IF-D95T). These can be powered by a battery or a small power supply. I am not responsible for any damage that may result from other people's implementation of these circuits. However, note that if correctly constructed both designs allow the scanner to be electrically isolated from your hardware. This should ensure that your scanner can never be damaged by your PC. Specifically, both circuits make sure that the signal between the scanner and the PC is an optical pulse, not a direct electrical signal. For example, if the scanner generates an electrical signal, I use a PC815 photocoupler to isolate the two systems. For these circuits, you should connect the 'OUT' pin the data logging computer's pin 11 and the circuit ground to the data logging computer's pin 19 (as described in the previous section). With all Philips scanners and Siemen's EPI scanner sequences prior to 2002B you will want to use the circuit for an electrical signal. For recent Siemens systems, you should use the circuit for the optical signal. The Siemens manaul 'Triggersignal outputs programmed by sequences' includes more details, as well as an alternative circuit for converting an optical pulse to a TTL pulse (my circuit is less expensive and also lengthens the duration of the optical pulse). An alternative Siemens optical circuit is described on the University of Liverpool MARIARC website

Schematic for use with Philips scanners

Schematic for use with Siemens scanners - signal from pin 6 can be used for TTL pulse to computer port or pin 7 can be used for a relay (note pin 7's pull down can provide more current than pin 6's push up).

Alternatively, you can set the scanner to generate longer pulses. I do not recommend this solution: increasing the scanner pulse length appears to decrease the speed of acquisition (Philips Intera 10.3 software). To change the pulse width generated by the Philips Intera, open the 'Scan Utilities' button, select 'service mode', select 'Control parameters' and adjust line 7: the 'DYN: Synch pulse duration (ms)'. You may need to log into the scanner in 'GyroAcq' mode instead of the 'Intera' mode to make these changes.

Software

My ezlog software works with computers using the Windows operating system and having a parallel port. The software has been tested with WindowsXP, but should work with Windows 95 and later. The software employs the Windows API Multimedia Timer that should offer millisecond accuracy on most computers. Because Windows is a multitasking operating system, it is possible that the software may ocassionally be off by a couple milliseconds, but the resolution is fine for measuring fMRI and behavioural data (the changes in blood flow occur over seconds). You can download my software by shift+clicking here. Simply unzip the file and run the software. Note that there are two files: the application 'ezlog.exe' and the library 'inpout32.dll': these files should remain togehter in the same folder on your hard disk. Double click on ezlog.exe to launc the program.

The first time you run the program, check that the parallel port address is set correctly. From your Windows Device Manager find out the address of your LPT port. The device manager reports the address as hexadecimal, and my software expects the value as decimal. You can use the scientific mode of the Windows caluclator to convert between the two. For example, if your LPT port has address $378, the decimal value is 888. Launch ezlog and choose Setup/SetPort and enter the correct address. You should only need to do this once, the software should remember your port address.

To start recording data, press the red 'start recording' button. The status bar on the bottom of the program's window will initially report 'Recording... waiting for 1st pulse'. As soon as the software begins detecting TTL pulses from the scanner it will begin showing the type of input and the time of input it is receiving. The window on the right shows a brief recording session: note that it registered pulses from the scanner every 2 seconds (e.g. pulses at 0, 1993, etc milliseconds). Note that the software also reports the onset of other events that were reported by the stimulus presentation computer (for example, it measured the 'E6' event type 3395ms after the first scanner pulse. To record a data sequence, you would want to follow the steps below: Prepare your scanner. Prepare the experimental software and have it ready to be triggered when the scanner starts. Press the 'start recording' button on ezlog. Start the scanner's fMRI recording. When the session is finished, press the 'Stop recording' button on ezlog. Press the 'Save to disk' button on ezlog to store the event files.

My ezlog software will save data in the '.csv' format (comma separated values). You can view csv files with any text editor, or you can open them with a spreadsheet, such as Microsoft Excel or the OpenOffice spreadsheet. The figure on the right shows the data for the logging session illustrated above. For example, row 4 shows that scanner pulses were recorded at 0, 1993, 3996... milliseconds. Row 3 summarises the scanner pulses, noting that the mean time between these pulses was 1999.556 milliseconds. This value would be the 'interscan interval' you would want to record if you were conducting an SPM analysis. Note that events recorded from the stimulus presentation computer are recorded both in terms of milliseconds as well as scans. For example, row 8 shows that 'E3' events were recorded at 7000 and 14200 milliseconds. While row 15 shows that these same events happened after 3.5 and 7.1 scans had elapsed (the start of the first scan is considered time zero). In programs like SPM2, the timing of events is typically coded in terms of the number of scans that have elapsed.

Notes:

• My ezlog software can record up to 15 different types of events from the stimulus presentation computer (4 bits, with 0 being used to denote the offset of an event).
• My software assumes that the data logging computer has its parallel port at address 888 decimal (hex 378). To check the address of your parallel port, right click on the 'My Computer' icon on the desktop and select properties, click on the 'Hardware' tab, click on the 'Ports' icon and right click on the Printer port' icon to select its properties. The 'resources' tab will show you the 'I/O range' for the parallel port. If this is not 0378-037F, you will want to uncheck the 'use automatic settings' checkbox and select a setting from the 'Settings based on' pull down menu that cause the I/O range to be 0378-037F.
• By default, the TTL pulse generated by the Philips Intera scanner is very brief (0.005ms). Since my software only checks the parallel port once per millisecond, you will want to increase the dynamic synchronization pulse width. Contact your Philips service people for details on how to do this (it is easy, as the changes can be set in software).
• You will also want to instruct your stimulus presentation computer to send TTL pulses at the onset and offset of each event. This will vary depending on the software you use. For EPrime or IFIS you have two options. The first option is slightly more accurate and also slightly more elegant. For both options, you will want to save a value between 1 and 15 that reflects the condition. I usually put this into the same list that selects the stimulus and correct response.For example, in addition to a column labelled 'CorrectResponse', you will want a column labelled 'PortOut' that has a different value between 1 and 15 for each condition. Only use ONE of the two following techniques
  1. You need to know the LPT port address for the EPrime computer. You can find this out using the Windows device manager. In the examples below I assume that this address is &H378 (hexidecimal 378; which is decimal 888). In Atlanta, our parallel port is &HE800 (hex E800).
  2. Change the properties of the object you wish to log to reflect the TTL pulse you want to record. For example, if you want to have the ImageDisplay object named 'TargetImage' trigger a TTL pulse, you could make the following changes:
     • Create an 'Inline' event that occurs before the stimuli are presented.
     • Add the following lines to the inline code:
       • TargetImage.OnsetSignalEnabled := true
       • TargetImage.OnsetSignalPort := &H378
       • TargetImage.OnsetSignalData := c.GetAttrib("PortOut")
       • TargetImage.OffsetSignalEnabled := true
       • TargetImage.OffsetSignalPort := &H378
       • TargetImage.OffsetSignalData := 0
  3. Add an inline code immediately before your target is presented. Set this to read "WritePort &H378, c.GetAttrib("PortOut")". Create a second inline code after your target and set this as follows: "WritePort &H378, 0". Note the first inline code switches on the TTL pulse, the second turns it off.
• You can also install my ezlog software on your stimulus presentation computer. This allows you to check that the cable is set up properly. Open copies of ezlog on both computers, and select 'Test and defaults' from the 'Setup' menu on both computers. When you click on the first four Parallel Port Output checkboxes on the stimulus presentation computer you should see the corresponding changes in the 'Inputs' checkboxes of the data logging computer.
• You can change the names for the different events.By default, and in the illustrations above, the 15 possible events are labelled 'E1', 'E2'...'E15'. However, it is probably easier to give the events meaningful names like 'LeftImage', 'RightImage', 'TopImage'. To change the event titles, open ezlog and select 'Test and defaults' from the 'Setup' menu. You will notice that there are 15 editable text boxes, initially called 'E1', 'E2', etc. My software will remember your labels between sessions. You can also make different copies of the software with different filenames (e.g. 'ezlog.exe', 'ezlog2.exe') and each will store and remember different event labels.
• Note that you can also start an EPrime experiment using a TTL pulse from your scanner. This allows you to synchronize the presentation of stimuli with your scans. You could use the "ReadPort" command. My BasicParallel experiment shows a simpler method:
1. Open your EPrime experiment, select 'Experiment' from the 'Edit' menu. Choose the 'Devices tab'. Press the 'Add' button and then create a 'Port' device. You will want to set the Collection Mode to "Presses and Releases", the Address to 889 (assuming that your parallel port is at address range 0378-037F hex [888-895 decimal], For example in Atlanta our address range is E800-E807 hex [59392-59399 decimal] so you in Atlanta use 59393 instead of 889), the size to 8, set "Invert" to yes, the Mask to 255, and "Emulate Device" to none.
   
2. At the start of your experiment you will want an ImageDisplay or TextDisplay object that will pause until a scanner pulse is detected. You will want to open this object's properties window and choose the "Input/Duration" tab. Set the duration to "(infinite)", the "End action" to terminate. For the Devices, add the port you created in the step and set the allowable input for this device to {ANY}. I also like to add a 'Keyboard' device, and set its allowable input to {F6}. This allows you to start the study without a pulse from the scanner by pressing Fn6 (identical to IFIS).
   
   
• If you want to use the scanner signal to trigger EPrime as well as use my datalogger, you will have to make a cable that looks like this: