Run custom sequences - josalggui/MaRGE GitHub Wiki

Step-by-Step Tutorial for Running a Custom Sequence

Running a custom sequence within the GUI involves several steps to ensure a smooth workflow and accurate data acquisition:

Step 1: Prerequisite - Autocalibration and Localizer

  • Perform Autocalibration and Localizer: Before running a custom sequence, complete the Autocalibration and Localizer processes.

Step 2: Localizer Completion

  • Console Message: Once the Localizer sequence is finished, a message will appear in the console (7), and the item corresponding to the localizer in the waiting list will update with its full name.
  • View Image:
    • Left Double-Click: To view the image, left double-click on the corresponding item in the waiting list.
    • Right-Click Menu: For viewing multiple images, use the right-click menu.
  • Adjust FOV:
    • In the image widget, click the FOV button to display a square representing the FOV for the next image. Adjust the size, position, and angle (under development) using the mouse.
    • Automatic Update: The corresponding values in the sequence list will automatically update. It's recommended to adjust the FOV this way to ensure it applies to all sequences.
    • Manual Entry: Typing FOV values directly in the text box will only affect the selected sequence.

Step 3: Sequence Selection and Modification

  • Select Sequence: Choose an image sequence (RARE, GRE, or PETRA).
  • Modify Parameters: Adjust the sequence parameters as needed to fit your imaging requirements.

Step 4: Running the Sequence

  • Run or Queue Sequence:
    • Acquire Button : Click the Acquire button to run the sequence immediately (this will freeze the GUI until the sequence completes).
    • Sequence to List Button : Use the Sequence to List button to add the sequence to the waiting list. This allows you to continue programming the next image while others are being acquired. This is the best way to run a sequence.
  • Completion Message: When the sequence finishes, a message will appear in the console. You can then view the results in the image area.

Sequence Parameters Categories

  1. RF: Parameters related to the RF signal, such as pulse amplitude, frequency, or duration.
  2. Image: Parameters related to the image, such as the field of view or matrix size.
  3. Sequence: Parameters related to contrast, such as echo time or repetition time.
  4. Others: Other relevant parameters, such as gradient rise time or dummy pulses.

File Management

  • Automatic Save: Each time a sequence is run, it saves a file in experiments/parameterization/SequenceName_last_parameters.csv.
    • Session Continuity: When you initialize the GUI, it loads parameters from these files to continue the session where it left off.
  • Generated Files: Running a sequence creates four files in experiments/acquisitions inside the session folder:
    1. Raw Data File: A .mat file named SequenceName.year.month.day.hour.minutes.seconds.milliseconds.mat containing inputs, outputs, and other useful variables.
    2. Input Parameters File: A .csv file named SequenceNameInfo.year.month.day.hour.minutes.seconds.milliseconds.csv. This file can be used to repeat an experiment by loading the parameters into the corresponding sequence using the Sequence/Load Parameters menu.
    3. Dicom File: A .dcm file in Dicom Standard 3.0 format.
    4. ISMRMRD File: A .ismrmrd file (coming soon).

By following these steps, you ensure a well-organized and efficient workflow when running custom sequences within MaRGE, leading to accurate and reliable data acquisition.## Step-by-Step Tutorial for Running a Custom Sequence