MRI Sequence Documentation: Localizer

Overview

The Localizer sequence is designed to quickly acquire low-resolution images along the three orthogonal planes (sagittal, transverse, and coronal) to aid in positioning and planning subsequent high-resolution scans.
This sequence inherits most of its configuration and functionality from the RARE PyPulseq base sequence, but introduces additional parameters for plane selection and readout orientation.

Sequence Description

The Localizer acquires a single low-resolution image for each selected plane.
It leverages the RARE sequence infrastructure, but is optimized for speed rather than high SNR or fine spatial resolution.

Key Components of the Sequence:

1. Plane Selection: The user can choose which planes to acquire: sagittal, transverse, and coronal.
2. Matrix Size: Typically small to reduce acquisition time. Must remain consistent with RARE sequence requirements.
3. Readout Direction and Axis Configuration: Allows control over the readout direction and axes for each plane, ensuring proper orientation of acquired images.

Parameters

The Localizer sequence inherits most parameters from the RARE sequence, with additional fields:

• Planes (sag, tra, cor): Select which planes to acquire. [1, 1, 1] acquires all three planes.
• RD Direction: Readout direction for each plane. Acceptable values are 1 (positive) or -1 (negative) for sagittal, coronal, and transverse.
• RD Axis: Specifies the readout axis for each plane (0=x, 1=y, 2=z).

All other parameters from the base RARE sequence (flip angles, repetition time, FOV, matrix size, echo train length, gradients, etc.) are still applicable and can be configured in the same way.

Important Notes:

• The Localizer sequence prioritizes speed over resolution; matrix sizes are typically smaller than diagnostic scans.
• Plane selection allows flexibility in image planning, but the axes and RD directions should be consistent with downstream high-resolution acquisitions.
• The sequence can be executed in Standalone mode, using the run_recon method, which will display the acquired planes and optionally save them.

SequenceRun and SequenceAnalysis

sequenceRun:

The sequenceRun method handles the acquisition for the selected planes. It loops over each plane, applies the proper readout direction and axis, and executes the base RARE sequence logic for data collection.

sequenceAnalysis:

Once the data is acquired, sequenceAnalysis processes each plane separately:

1. Fourier Transform: Converts k-space data to image space.
2. Reconstruction: Each plane is reconstructed using the RARE pipeline. Tyger reconstruction or denoising can be applied if enabled.
3. Post-processing: Cropping, orientation correction, and plotting are applied for visualization.

Output and Results

• The Localizer produces one 2D or 3D image per selected plane.
• Images are oriented according to the specified RD axis and direction.
• Data can be exported in standard formats (DICOM, NIfTI) for planning purposes.
• Intermediate k-space and reconstruction logs are stored similarly to the RARE sequence.

Raw Data

• planes: Binary flags for sagittal, transverse, coronal planes.
• rd_directions: Readout direction for each plane.
• rd_axis: Readout axis for each plane.
• All inherited RARE parameters: Including rfExFA, rfReFA, nPoints, FOV, dummyPulses, etl, etc.