Run scanning session

Running the scanning session¶

Prepare the visual stimulation experiment¶

Click here to check out the psychopy code for the 2.0 MR-Eye study, and here for the MR-Eye Track study

At the end of the ET calibration we are ready to continue with the experiment.
Wait for the sentence regarding the initial description of the task: “In this task you will see...”
Now, get ready to prepare the scanning sequence (next step).

Prepare the scanning sequence¶

Copy the Pulseq (.seq) files¶

If you are using Pulseq to develop your own sequences, the first thing you'd need to do is to copy your .seq files into the corresponding Siemens folder for Pulseq, in C:\ProgramData\Siemens\Numaris\MriCustomer\CustomerSeq\pulseq, as shown in the picture below.

pulseq-folder

Add a new patient¶

First, register a new patient, completing the last name, the name, the patient ID (you can press the Tab bar and the field will be automatically filled by the current timestamp), date of birth, age (automatic after entering the date of birth), sex, height and weight. On the right of the UI, open the Program Selection window to choose your protocol. If you don't have one yet, it is recommended to create one, so every time you scan a new subject, you don't have to drag and drop all the sequences, they will already be there! Select "Any Polarization" as RF Transmit Mode. Select "Brain" as Body Part and Laterality. Select "Head First Supine" as Patient Orientation. You're good to go!

idea-patient

The protocol includes several sequences. In DEBI protocol's case, a head-scout, a high-resolution anatomical image (MP-RAGE), and other sequences depending on the project: T1w-LIBRE for MR-Eye Track and T1w-LIBRE, T1w-VIBE, T2w-LIBRE, and T2w-TSE for 2.0 MR-Eye.

Load the Pulseq (.seq) files¶

Once you have run the scout and the MP-RAGE, and you have positioned the FOV accordingly (check the video recording below), load the .seq file by going to Sequence > Special.

Change "libBalance / Grad health" to "disabled"

Disable the "libBalance / Grad health" before loading the sequence. Otherwise, the UI might freeze...

Select your sequence from the Pulseq file list
Change "Timing and Flip Angles" to "strict"
Leave the rest of the parameters untouched
Adjust the FOV and Shimming box (check the video recording below)

pulseq-load-sequence

Modify some system parameters¶

Go to System > Coils and modify the following:
- Select HC1 to HC7 (all of them, in the video recording it is only shown HC3 to HC7, when the video was recorded)

idea-coils

Go to System > Miscellaneous and modify the following:
- Coil selection: Manual
- Coil combination: Sum of Squares
Go to System > Adjustments to:
- Adjustment strategy: Standard
- B0 Shim: Standard
- B1 Shim: Patient-specific
- Adjustment Tolerance: Auto
- Disable "Adjust with Body Coil"

idea-adjustments

Send the trigger to both the scanner and the stimuli laptop¶

In IDEA UI, go to Physio, and select EXT Trigger.

idea-ext_trigger

Then, when the scan is launched through the Syncbox, you should see something like the following screenshot (make sure you have activated the Physio display with External Signal I):

idea-triggers

Video recording of the whole process¶

Your browser does not support the video? Click here to download it.

How to acquire prescans¶

You can refer to this link documentation of monalisa reconstruction where we explained with a video recording how to do acquire the prescans: Prescan Acquisition Guide. Remember to enable "Adjust with Body Coil" in System > Adjustments (only for prescans).

Session Completed¶

At the end of the stimulation, click “t” on the experimental laptop and click the round button on the SyncBox to stop the running session.
The exam is over, inform the participant that the session has concluded.
You can proceed with the tear-down protocol.