Run custom sequences - josalggui/MaRGE GitHub Wiki

Step-by-Step Tutorial for Running a Custom Sequence

Running a custom sequence in the GUI involves several steps to ensure a smooth workflow and reliable data acquisition.

Step 1: Prerequisite — Autocalibration and Localizer

Before running any custom sequence, complete both:

  • Autocalibration (Required)

  • Localizer (Recommended)

These steps ensure the system is fully prepared for accurate imaging.

Step 2: After Localizer Completion

  • Console Notification: When the Localizer finishes, a message appears in the console, and the corresponding item in the waiting list updates to its full name.
  • View Images:
    • Left Double-Click the item in the waiting list to view the image.
    • Right-Click Menu to conveniently browse multiple images.
  • Adjust the FOV:
    • In the image widget, click the FOV button to display a square representing the FOV of the next image.
    • Resize or reposition the FOV using the mouse.
    • Automatic Update: All related FOV fields in the sequence list update automatically. This is the recommended method.
    • Manual Input: Entering FOV values directly in the text box affects only the selected sequence.

Step 3: Sequence Selection and Modification

  1. Select the desired imaging sequence (e.g., RARE, RarePyPulseq, RareDoubleImage, GRE, PETRA).
  2. Adjust parameters to meet the requirements of your specific imaging task.

Step 4: Running the Sequence

You can run a sequence in two ways:

  • Acquire Button Runs the sequence immediately. The GUI will freeze until the acquisition finishes.

  • Sequence to List Button Adds the sequence to the waiting list, allowing you to continue setting up additional images while others are being acquired. This is the preferred method.

A completion message will appear in the console when the sequence is done, and the resulting images will be displayed.

Sequence Parameter Categories

  1. RF — Pulse amplitude, duration, frequency, and related RF settings.
  2. Image — Field of view, resolution, and matrix size.
  3. Sequence — Contrast parameters such as TE, TR, and echo train settings.
  4. Others — Additional controls, including gradient rise times, dummy pulses, and auxiliary settings.
  5. Tyger — (NEW) Tools related to reconstruction and Tyger.

File Management

Each time a sequence is executed, several files are automatically created to ensure reproducibility and proper record-keeping.

Automatic Parameter Save

A .csv file is stored in:
experiments/parameterization/SequenceName_last_parameters.csv

  • These files allow the GUI to reload the last-used parameters at startup for session continuity.

Generated Files

Running a sequence produces four files inside the session folder under:
experiments/acquisitions

  1. Raw Data File (.mat)

    • Contains inputs, outputs, and auxiliary variables.
    • Filename format:
      SequenceName.YYYY.MM.DD.HH.mm.ss.mmm.mat

  2. Input Parameters File (.csv)

    • Filename format:
      SequenceNameInfo.YYYY.MM.DD.HH.mm.ss.mmm.csv
    • Can be reloaded using Sequence → Load Parameters to repeat an experiment.

  3. DICOM File (.dcm)

    • Saved in DICOM Standard 3.0 format.

  4. NIFTY File (.nii)

    • Saved in NIFTY format.

  5. ISMRMRD File (.ismrmrd)

    • Coming soon.

  6. A copy of the hardware configuration files

Sequece workflow