This page describes the TMS system at the University of Arizona. This equipment belongs to the Chou lab. To request access, contact Ying-hui Chou (yinghuichou at email.arizona.edu) to discuss your proposal. The equipment resides in a locked room in the basement of the BSRL, down the hall from the MRI scanner.
If you find inaccuracies (or typos or broken links), please let me know: dkp at email.arizona.edu. The descriptions provided below are based on extensive and excellent lab manuals prepared by Yu-chin Chen and Aneta Kielar. This page should provide you with a good sense of how you might proceed in a typical study, but it is not meant to be exhaustive. There is, for example, a 200+ page manual on the TMS-Navigator software (sorry, this is proprietary and cannot be posted).
It might be helpful to have some kind of TMS Checklist. The linked one is in Word format so you can edit it to add or remove the details you need.
A short (3.5 minute) TMS Experience movie is available to show potential participants what it is like to get set up for TMS.
Want PDFS? Read the Docs has the ability to output documentation in other formats: pdf and epub. On the bottom left it says
Read the Docs v:latest. Under
Downloads, choose one of the
latest options (e.g. PDF). The PDFs have much nicer formatting than if you simply “save as” pdf in your browser. The only downside is that the pdf includes everything on the website, so you’ll want to use Preview or Adobe Acrobat or something similar to extract the portion of the documentation you want. Of course, you could just print the range of pages you want as hard copies.
To use the TMS (Transcranial Magnetic Stimulation) for research, we rely on three separate hardware systems. Here they are:
Localite Computer and Camera
Left: The C-B60 coil being attached to the MagPro; Right the same coil being detached from the MagPro.
Once per Project: Folders and MNI Planning¶
To create and edit MNI planning scenarios, a session does not have to be started or loaded, and the tracking system and instruments are not required.
Create a folder on each computer (Localite and MEP) to store participant data for your lab.
On the Localite computer, use MNI Planning to create one or more lists of stimulation targets in standard space:
Subsequently you can load these saved targets (You can always edit this later if necessary).
Now you are somewhat familiar with the TMS hardware and the TMS Navigator software. Hopefully, you have set up MNI Planning. Now you can proceed to actually set up and run a participant. In the flowcharts below, clicking a node with a blue border will take you to the relevant section. Hardware=pink. Physical activities=cyan. Localite software=grey. MEP software=green. If order does not matter, a dotted line is used as a connector.
Before Participant Arrives¶
After Participant Arrives¶
Spike2 Setup (MEP computer)¶
Click the Spike2 icon to start the program. Spike2 is used to track muscle contractions from the electrodes you will place on the participant’s hand.
New Data Document¶
For each session, create a new Data Document:
Click the Spike2 icon on the MEP computer desktop.
File ➜ New ➜ Data Document ➜ OK
Apply Resource File¶
If the script bar is not visible, then select Script ➜ Script bar from the menu
Click View ➜ Toolbar (this shows us the Start and Stop buttons we want later)
Press TMS-EMG on the Script bar
Start Time: Cursor 1
End Time: Cursor 2
Measurement: 10 Peak to Peak
Cursor 1 and Cursor 2 may not be visible after hitting okay. Don’t worry, they are present but hidden.
Create a participant folder. This is where we will eventually save output from the main Spike EMG Reading window and the Log window.
Set up Session (Localite computer, Toolbar)¶
Optimally, you should have a T1-weighted scan with ~1mm isotropic voxels. You have several options for providing an anatomical scan (choose only one option, usually DICOMS):
Bring DICOMS direct from the scanner
Bring a Nifti volume
If your participant is returning for additional sessions, you can load a bookmark from the planning you did last time. From the Menu, choose Load previous bookmark in New Session. This will allow you to skip ahead to participant setup. By loading the bookmark in a new session, you will have a separate folder for each session, which makes data mangement cleaner.
If you don’t have a scan, you can use the standard MNI scan available in TMS-Navigator
1TMS Navigator looks for a folder named DICOMDIR in your Patient Folder and will show you the DICOM images within it.
2, ensure that a folder containing the NIFTI anatomical file(s) is available.
Load Anatomical Image: Option 1 DICOMS¶
In general, you will load anatomical images directly from the scanner. This means they will be in DICOM format. TMS Navigator is specially suited to working with DICOM images.
Load Anatomical Image: Option 2 NIFTI¶
Enter Patient Demographics¶
Regardless of whether you loaded DICOMS or NIFTIs, you need to check that your patient demographics information is correct.
If you do not select a patient from the patient list, TMS Navigator will create a second individual patient folder! This is true even if the patient already exists and even though the correct information is displayed in the Patient Data section! So, make sure you choose your patient from the patient list at the top (unless it is really a new patient).
Patient Registration Landmark Setup (Toolbar)¶
In addition to surface registration, specific landmarks help the software track location accurately
Define Registration Markers (upper right in figure below): Marker List
+for each new marker:
(1) L_ear, (2) L_eye, (3) Nasion, (4) R_eye, and (5) R_ear
Double check colors and locations.
Cancel (Because the participant is not here to be registered).
Brain Segmentation (Toolbar)¶
Brain segmentation creates a 3D image of the brain which is useful for placing the grid correctly during Talairach definition. The brain segmentation also provides us with a nice view of the sulci and gyri of the brain which facilitates locationg targets.
Click the cursor in the middle of a large region of WM ➜ Calculate (red rectangle).
If the cerebellum and/or spinal cord is not included, click each and calculate again.
Try Defaults, else Range=7-34; Sensitivity=12.
Increased range ➜ Increased coverage
You can reset segmentation and start over.
Brightness and Contrast (Lower Control Area)¶
Adjust window width (contrast) and window center:
Reduced width (range) ➜ increased contrast
Decreased center ➜ increased brightness
Peel surface (Lower Control Area)¶
If gyri/sulci are cloudy then peel the brain surface (~3mm)
Load MNI Planning Targets¶
Now that the participant’s brain is registered to standard space, you can load a saved MNI Planning list, e.g., File ➜ MNI Planning ➜ Kielar lab ➜ Load (Load standard space targets)
Rotation and Entry for each Target¶
For each target defined with MNI planning, we need to know the corresponding location for stimulation on the surface of the head.
In the lower control panel:
In the Planning Control Panel:
Check Define rotation.
Set rotation to 45 degrees in the left hemisphere and 315 degrees in the right hemiphere.
Click Calculate Entry in the Planning panel.
If you have reason to set a different rotation value, you certainly should, but the above values are typical.
The Hand Knob¶
Set up Participant¶
Paperwork Explain the study, have the participant read and sign any consent forms, and fill out the MRI and TMS safety screening forms. Double check for contraindications!
Provide earplugs to the participant to protect their hearing from the noise of the coil.
Place a reference tracker on the participant’s forehead. The reference tracker is available in two forms: a stick-on version, and a headband version. In general, the stick-on reference tracker is to be preferred as it is better tolerated and more reliable. Depending on the stimulation site, you might have to use the headband (if it is not possible to place reference on forehead). If using the headband, make sure it is not too tight (can cause headaches) and not too loose (can cause the reference tracker to shift).
Electrodes are placed on the participant’s hand to establish the motor threshold. Choose the correct hand (e.g., the right hand if we are stimulating the left hemisphere.
No matter the selected muscle, place electrodes as follows: red = muscle belly, white = tendon/bone (lateral face of selected finger), black = bony protuberance of ulnar head for grounding. Before placing the electrodes, you can ask the participant to flex the targeted muscle while palpating the muscle belly. You should feel the muscle contract (contracted muscle = firm), which will inform optimal placement of the muscle belly electrode. For the APB, illustrated here, have the participant repeatedly touch the thumb to the pinky to find the muscle belly.
Demonstrate the pulse at lower intensity (30) on participant’s arm (as long as there is no metal in the arm) and then the head (45).
Ask them to relax their hand.
Resume Patient Registration¶
Now that the participant is here and has a reference tracker affixed, we need to yoke the real world landmarks and head surface to the MRI data in TMS Navigator.
The display contains four equal sized panels. To change the layout, choose View ➜ Layout in the menu. For example, you can maximize the size of panel 4 to make it easier to see the 3D representation.
Point to each landmark on the participant with the pointer (guide the pointer with your finger, covering the tip to prevent slipping/unwanted contact). The pointer location needs to match the landmarks on the MRI scan. For example, the specified landmark location for the left ear may vary by operator (always aim for left tragus). Ensure consistency between the marked target on the MRI scan and pointer placement. Use the 3D head image as a guide.
Place the pointer on head ➜ Blue footpedal down ➜ Drag ➜ Blue footpedal up ➜ pointer off head.
Repeat in several directions, left & right (100-300 points).
Get extra registration markers over the eventual stimulation site.
Be careful not to push too hard as this can cause discomfort. You want to keep contact with skin, but just lightly tracing the pointer rather than pressing firmly.
Click Next (green button) when you are finished adding points to recalculate the RMS.
To accept the new RMS, click OK .
To reject the new RMS, click Previous, Next and No. This should allow you to add more data to the surface registration.
Hold the pointer so it is touching the head and perpendicular to it. You should see no gap between the pointer and the surface of the head (2D views).
Calibrate the coil to ensure it is recognized by the camera.
Instrument selection ➜ Coil 1 (MagVenture C-B60)
Place the calibration board on the coil and hold it near the participant.
Tip the board and coil so the camera can see all the reflector balls.
Calibrate Coil 1…
Check Camera (Polaris Spectra P7) Position (Toolbar)¶
Set up to Find Motor Hotspot¶
We have set up the equipment and the participant. We have planned our targets and entries.
We are going to stimulate the hand knob, and subsequently revise the location of the hand knob using an instrument marker from successful stimulation.
We’ll need the four control panels described below.
Stimulation (Lower Control Area)¶
If you forget to choose Update during recording never fear. The stimulation markers are still being created, you just won’t see them populate the list right away. But, you should see them when you press Stop.
Choose Entry/Target (Lower Control Area)¶
On the MagPro screen, ensure the coil is correctly identified as the C-B60 (the small coil). Turn the Options Wheel to
A. Select Recall. After selecting Recall, the details of your sequence are displayed in the information area on the left:
Setup View A. You may use the Amplitude Wheel and Enable/Disable button if you prefer these to the Stimulator panel.
When you enable the coil, amplitude is reset to
0! You will need to set amplitude to
55 when you try to locate the motor hotspot. If you switch between different methods of setting the amplitude (dial on C-B60 coil, MagPro amplitude wheel and stimulator control panel), the amplitude may jump when you switch back to the previous method. Be cautious about this.
The Motor Hotspot¶
Locating the motor hotspot requires TMS-Navigator on the Localite computer and Spike 2 on the MEP computer.
Establishing the RMT additionally requires Pest on the MEP machine.
Start Sampling with Spike 2¶
Adjust the Y-axis (Spike 2)¶
Locate the Motor Hotspot¶
Set the amplitude to
30. The amplitude can be set in at least 3 different ways:
Using the dial on the C-B60 coil
Using the amplitude wheel on the Magpro
Using the Stimulator control panel in TMS Navigator
Demonstrate the coil stimulation on the participant’s arm at amplitude=
30(as long as there is no metal in the arm), and head at amplitude=
Set the amplitude=
55, then navigate to the handknob and stimulate it. You may have to move the coil around to find the correct spot.
Watch the participant’s hand. The thumb, and not some other part of the hand, should move.
Often this is right where we placed the handknob target, but if that isn’t right, we need to move the coil around a bit and try stimulating nearby areas.
Occasionally someone has a higher threshold and you’ll need to increase the amplitude to stimulate the hotspot (e.g., we’ve seen amplitudes of 75 or even 80, but this is uncommon).
When you find a robust thumb twitch, press Stop on the stimulation control panel. We are done recording:
In the Navigation control panel, choose Instr. Marker Navigation to navigate using the instrument marker we just created.
Now that we have identified the motor hotspot, start Pest. Pest is a motor threshold assessment tool. Pest runs some clever algorithms to help choose the optimal stimulation threshold. We will use Pest to stimulate the identified motor hotspot from the previous step.
Test Threshold for 3/6¶
After identifying Pest’s guess at the motor threshold, ensure that 3/6 stimulations at that intensity produce a twitch.
If we get too few responses, increase the threshold by
1and try again.
If we get too many responses, decrease the threshold by
1and try again.
If you get
4/6and then decrease and get
2/6, then your final value is the
After we establish the RMT we calculate 70% of that value. 70% of RMT will be our TBS intensity for both cTBS and iTBS.
Spike2: Quit and Stop (Do NOT close)¶
When recording is stopped, it cannot be resumed. We will wait until later to save the MEP data.
Remove electrodes from participant
For now press the quit button (illustrated in the figure) and the stop button on the Toolbar.
Later, when we finish the session we will save data from Spike.
For now, you must not close Spike.
TBS (Theta Burst Stimulation)¶
It is time to change the coil from the small C-B60 to the large Cool-B65 we will use for TBS. As soon as you unplug the small coil, the Localite computer will prompt you to switch or keep calibration. It does not matter what you select, or if you ignore the prompt until the large coil is plugged in.
Ensure the cooling unit is on.
You are going to apply either iTBS which increases cortical excitability or cTBS which decreases cortical excitability.
Check the positioning of the coil tracker balls to ensure they won’t be in the way while you are applying the stimulation to the participant. You can move them but you should do so before you calibrate the coil.
Calibrate the coil. This time choose Calibrate Coil 2. The calibration screen should recognize that the coil is now the Cool-B65.
Apply the coil setup instructions to Coil 2 (the Cool-B65)
On the MagPro screen press the Main button.
Main will be replaced by the Timing on the bottom left of the screen.
Turn the knob to
Yfor iTBS or
Cfor cTBS. Press Recall.
Press Timing to see the timing details. The
START/STOPsoftkey on the lower right is enabled. Now the pulse train can be triggered from the Stimulator panel using the Start/Stop Train button
Navigate to the target of stimulation (something other than the hand knob, we presume).
The Cool-B65 coil is heavy which makes it difficult to hold steady for the requisite amount of time. The heavy coil may also tend to move the participant’s head as it rests against it. You may find it helpful to have the participant use the chinrest (there is a soft blue squishy disk to make it more tolerable).
Wrap Up the Session¶
You want to save data from both the Localite and MEP machines to your external device.
You also want to turn off hardware.
Localite Data Save the participant folder you created earlier to your external device. MEP Data Save data from Spike2 and Pest to your external device.
Save Main EMG Reading Window: Make sure that the focus is on the main EMG Reading Window and click Save in the upper left to save it to the appropriate participant folder. If the file has the *.smr extension, then you know you saved the right window.
Save Log: Save the log by clicking in the log window and following the same steps (but the output will be a *.txt file).
Ensure that you have named both files using your protocol and that they are in the participant folder you created.
Copy the participant folder to your external drive.
You can close Spike2.
Save the Pest data to the participant folder.
Turn off Hardware¶
MEP Turn off the amplifier and data acquisition devices.
Coil Disconnect the large coil, and reconnect the smaller coil.
MagPro Turn off the Cooling Unit and MagPro.
Localite Computer Turn off Localite computer.
Order is not terribly important here. The MEP equipment is separate from the Coil/Localite/MagPro. It is probably best to turn off the Localite machine last (but I’m not sure why I say that).