This directory contains code for a Texas Instruments Hercules microcontroller board. The microcontroller and code are responsible for sending triggers to the MagVenture TMS unit and synchronizing these triggers with the Siemens MRI scanner. To use the Hercules microcontroller, which is a 3.3 Volt system and can be damaged by 5.0 Volt signals, you must first do a level shift of the 5.0 Volt TTL pulse issued by the scanner. You can find a circuit diagram and parts list on the wiki page associated with the GitHub Brain-Imaging-Center/TMS-fMRI repository.

The code does the following (Specifics are documented with the code.):

(I) Initializes the microcontroller (see sys_main.c). Hardware interrupts are configured, input/output ports are configured and the RTI clock is started.

(II) Reads a file called TMS_trig_data (see sys_main.c). This file is created by the user and controls the timing of the triggers sent to the TMS unit. The TMS_trig_data must be located in the TMS_trig_files subdirectory of the code. The file contains on each line: (1) The EPI volume number during which the trigger should be sent to the TMS unit, (2) The number of triggers in a train of triggers associated with that particular volume, and (3) The time (in microseconds) at which you would like the triggers in the train sent to the TMS unit relative to the MRI scanner TTL pulse associated with that volume. Please see TMS_trig_data_1 as an example. The TTL pulse from the scanner occurs prior to the MRI scanner's slice selection RF pulse. Please see the wiki page associated with this GitHub repository for more information about when the scanner TTL is sent relative to other scanner events.

(III) Receives the TTL pulse signal from the MRI scanner. This signal produces a hardware interrupt in the microcontroller (see the gioNotification() function in the file notification.c). The associated interrupt service routine (ISR) named gioNotification() does the following: (1) Counts these interrupts, (2) Sets the leading edge of the first rectangular 10 microsecond trigger pulse in the train of triggers associated with a particular volume designated in the TMS_trig_data file and (3) Schedules the trailing edge of the first trigger of the train of triggers associated with a particular EPI volume (This is done by using hardware interrupts associated with the real-time interrupt system of the microcontroller).

(IV) Schedules successive leading and trailing edges of the rest of the triggers in a train associated with a particular EPI volume. This is done by using using hardware interrupts associated with the real-time interrupt system of the microcontroller. See the rtiNotification() ISR in the sys_main.c file.

To run the code you will need to install Code Composer Studio (CCS) on a PC. CCS is available free of cost through Texas Instruments at http://www.ti.com/tool/ccstudio. You will also need to install the F021 API (downloaded spnc033.zip from http://www.ti.com/tool/f021flashapi). Then add the location of the include files to the project by right-clicking on the project then clicking project Properties -> Build -> ARM Compiler-> Include Options. Under "Specify a preinclude file" add the path to the F021.h header file. The path will look something like: C:\ti\Hercules\F021 Flash API\02.01.00\include\F021.h and you should substitute the path to the F021.h file on your machine.

Once the above installation steps are done you may download the code in this repository and place it in the directory you have choosen for your project files (you will see this directory when you start up CCS). Then start CCS and go to Project -> Import CCS Projects and use the browser to locate and select the Blinky project folder.

The sychronization of the TMS system with the MRI scanner is determined by the user by creating the TMS_trig_data file (mentioned above) and after creating the TMS_trig_data file the user can compile the code and load it to the microcontroller by doing the following:

(1) Open CCS.

(2) Right-click on the Blinky project directory (under the Project Explorer tab).

(3) Click Run->Debug

This will compile, erase and then load (flash) the code to the microcontroller. You must do this each time you run the code.

Having compiled and loaded the code to the microcontroller you may then run the code by clicking the green arrow button in CCS gui. The code will then read the TMS_trig_data file and, following completion of the read, you should see a message that says "Ready to send triggers to TMS unit" appear in the CCS console. After seeing that message you can click the red box near the green arrow and you are ready to go.