Sequences

Spintuition reads and writes Pulseq .seq files, so sequences can move between Spintuition and other MRI tools.

Open the Sequences panel with the sequence icon at the top of the Full View. Tap a sequence to review its description, duration and spin matrix before loading it.

Sequence library

Category	Contents
Basic	MRI fundamentals and introductory examples, bundled with the app.
Advanced	Complete and steady-state pulse sequences, bundled with the app.
My Sequences	Sequences you saved from the main view. Rename with the pencil icon, swipe left to delete, and drag to reorder with Edit.

• Loading a sequence replaces the current waveforms and spin matrix settings.
• Replace Waveforms turns off automatically on load, so the sequence is not accidentally overwritten.
• Load at Startup in the load dialog makes a sequence load at launch (only one at a time).
• After loading, use Back to Start to replay it from the beginning.

Import scaling

When loading a Pulseq file, the Pulseq Scaling controls adapt external sequences to Spintuition’s visualization. They are applied after the waveforms are loaded:

• Scale RF — RF amplitude (default 1.0)
• Scale Gx, Gy, Gz — gradient amplitude per axis (default 1.0)

Pulseq gradients are converted from Hz/m to kHz/m. By default they are also scaled by 1/50 so that realistic resolutions produce a few visible cycles across the 25 cm FOV (1/4 m). The SimmrGradScale directive replaces this default.

Note that at 25cm FOV, the scaling from kHz/m to kHz/FOV is just a division by 4!

Export

Share Waveforms on the Waveforms panel exports the current waveforms as a .seq file, including Simmr directives that restore the matrix and display state when it is reimported.

Writing sequences in MATLAB

The bundled examples are generated with the Pulseq MATLAB toolbox (see matlab_pulseq/). Directives can be added with setDefinition:

seq = mr.Sequence();
seq.setDefinition('#SimmrDescription', 'x Gradient: spins rotate at different rates depending on x position.')
seq.setDefinition('# SimmrMatrixSize', ' 5 1 1')
seq.setDefinition('# SimmrSpinInit',   ' x')
seq.setDefinition('# SimmrT1',         ' 100')
seq.setDefinition('# SimmrT2',         ' 40')
seq.setDefinition('# SimmrView',       ' obl')

gx = mr.makeTrapezoid('x', 'FlatArea', 20000*10e-3, 'FlatTime', 10e-3, 'system', sys);
seq.addBlock(gx);
seq.write('A2_x_gradient.seq');

Simmr directives

Spintuition reads optional app-specific directives from comments in Pulseq .seq files. Other Pulseq tools ignore these lines as ordinary comments. The prefix remains Simmr for file compatibility.

Syntax

# SimmrMatrixSize 5 5 3
# SimmrSpinInit z
# SimmrLabFrame off

• One directive per comment line. Directives may appear anywhere; placing them before [VERSION] makes them easier to find.
• Names are case-insensitive, and whitespace between # and the name is optional.
• A colon or equals sign may separate name and value; a space is canonical.
• Invalid or unknown directives are ignored. For single-value directives the last valid value wins.
• SimmrSpinInit and SimmrPause are repeatable and accumulate timed events.
• Unless noted, times are in ms and frequencies in kHz, matching the app controls.

Sequence information

Spin matrix and playback

Simulation settings

Vector display

Camera

Camera vectors are normalized when loaded, and the three separate vectors take effect only when all three are valid. Canonical presets:

# Axial — view along Z, X across, Y vertical
# SimmrCameraBasis 0 0 1   1 0 0   0 1 0

# Sagittal — view along X, Z across, Y vertical
# SimmrCameraBasis -1 0 0  0 0 1   0 1 0

# Coronal — view along Y, X across, Z vertical
# SimmrCameraBasis 0 -1 0  1 0 0   0 0 1

Compatibility aliases

SimmrTimeMultiplier appeared in older documentation but is no longer parsed; Pulseq timing is converted to Spintuition’s millisecond timeline automatically.

Full example

# SimmrDescription Slice-selective excitation example
# SimmrID 5C57AF74-61DE-4D4B-931D-994D77D34F8A
# SimmrCreatedAt 1791475200
# SimmrMatrixSize 5 5 3
# SimmrSpinInit z
# SimmrSpinInit x 12.5
# SimmrPause 8
# SimmrSS 4
# SimmrT1 40
# SimmrT2 10
# SimmrDf -0.25
# SimmrDfr 0.1
# SimmrGradScale 0.02
# SimmrLabFrame off
# SimmrShowB1 on
# SimmrFadeUnexcited 10
# SimmrAverageXYZ on
# SimmrAverageX off
# SimmrAverageY off
# SimmrAverageZ on
# SimmrTrail 1.5
# SimmrView obl

[VERSION]
major 1
minor 5
revision 0

You can download/modify the examples here.