From f2c268b56c1cbf1d852fa5d3168249b91646e310 Mon Sep 17 00:00:00 2001
From: Christoph Kolbitsch <christoph.kolbitsch@ptb.de>
Date: Mon, 16 Mar 2026 20:30:14 +0000
Subject: [PATCH 1/6] refactor trajectory

---
 src/mrseq/scripts/t1_molli_bssfp.py           |   2 +-
 src/mrseq/scripts/t2_t2prep_flash.py          |   2 +-
 src/mrseq/scripts/t2star_multi_echo_flash.py  |   4 +-
 src/mrseq/utils/MultiEchoAcquisition.py       | 203 +++++++++++++
 src/mrseq/utils/__init__.py                   |   4 +-
 src/mrseq/utils/cartesian_sampling.py         |  82 +++++
 .../{trajectory.py => spiral_sampling.py}     |   0
 tests/utils/test_cartesian_sampling.py        |  67 +++++
 tests/utils/test_multi_echo_acquisition.py    |  87 ++++++
 tests/utils/test_spiral_sampling.py           | 138 +++++++++
 tests/utils/test_trajectory.py                | 281 ------------------
 11 files changed, 584 insertions(+), 286 deletions(-)
 create mode 100644 src/mrseq/utils/MultiEchoAcquisition.py
 create mode 100644 src/mrseq/utils/cartesian_sampling.py
 rename src/mrseq/utils/{trajectory.py => spiral_sampling.py} (100%)
 create mode 100644 tests/utils/test_cartesian_sampling.py
 create mode 100644 tests/utils/test_multi_echo_acquisition.py
 create mode 100644 tests/utils/test_spiral_sampling.py
 delete mode 100644 tests/utils/test_trajectory.py

diff --git a/src/mrseq/scripts/t1_molli_bssfp.py b/src/mrseq/scripts/t1_molli_bssfp.py
index 5554778..471bfbe 100644
--- a/src/mrseq/scripts/t1_molli_bssfp.py
+++ b/src/mrseq/scripts/t1_molli_bssfp.py
@@ -6,11 +6,11 @@
 import pypulseq as pp
 
 from mrseq.preparations import add_t1_inv_prep
+from mrseq.utils import cartesian_phase_encoding
 from mrseq.utils import find_gx_flat_time_on_adc_raster
 from mrseq.utils import round_to_raster
 from mrseq.utils import sys_defaults
 from mrseq.utils import write_sequence
-from mrseq.utils.trajectory import cartesian_phase_encoding
 
 
 def t1_molli_bssfp_kernel(
diff --git a/src/mrseq/scripts/t2_t2prep_flash.py b/src/mrseq/scripts/t2_t2prep_flash.py
index 8f69521..78f9f0a 100644
--- a/src/mrseq/scripts/t2_t2prep_flash.py
+++ b/src/mrseq/scripts/t2_t2prep_flash.py
@@ -6,11 +6,11 @@
 import pypulseq as pp
 
 from mrseq.preparations.t2_prep import add_t2_prep
+from mrseq.utils import cartesian_phase_encoding
 from mrseq.utils import find_gx_flat_time_on_adc_raster
 from mrseq.utils import round_to_raster
 from mrseq.utils import sys_defaults
 from mrseq.utils import write_sequence
-from mrseq.utils.trajectory import cartesian_phase_encoding
 
 
 def t2_t2prep_flash_kernel(
diff --git a/src/mrseq/scripts/t2star_multi_echo_flash.py b/src/mrseq/scripts/t2star_multi_echo_flash.py
index e73638e..46494a4 100644
--- a/src/mrseq/scripts/t2star_multi_echo_flash.py
+++ b/src/mrseq/scripts/t2star_multi_echo_flash.py
@@ -6,6 +6,8 @@
 import numpy as np
 import pypulseq as pp
 
+from mrseq.utils import MultiEchoAcquisition
+from mrseq.utils import cartesian_phase_encoding
 from mrseq.utils import find_gx_flat_time_on_adc_raster
 from mrseq.utils import round_to_raster
 from mrseq.utils import sys_defaults
@@ -14,8 +16,6 @@
 from mrseq.utils.ismrmrd import Limits
 from mrseq.utils.ismrmrd import MatrixSize
 from mrseq.utils.ismrmrd import create_header
-from mrseq.utils.trajectory import MultiEchoAcquisition
-from mrseq.utils.trajectory import cartesian_phase_encoding
 
 
 def t2star_multi_echo_flash_kernel(
diff --git a/src/mrseq/utils/MultiEchoAcquisition.py b/src/mrseq/utils/MultiEchoAcquisition.py
new file mode 100644
index 0000000..7c5ab9d
--- /dev/null
+++ b/src/mrseq/utils/MultiEchoAcquisition.py
@@ -0,0 +1,203 @@
+"""Basic functionality for trajectory calculation."""
+
+import numpy as np
+import pypulseq as pp
+
+from mrseq.utils import find_gx_flat_time_on_adc_raster
+from mrseq.utils import round_to_raster
+from mrseq.utils import sys_defaults
+
+
+class MultiEchoAcquisition:
+    """
+    Multi-echo gradient echo acquisition.
+
+    Attributes
+    ----------
+    system
+        PyPulseq system limits object.
+    n_readout_post_echo
+        Number of readout points after echo.
+    n_readout_pre_echo
+        Number of readout points before echo.
+    n_readout_with_partial_echo
+        Total number of readout points with partial echo.
+    te_delay
+        Additional delay after readout gradient gx to achieve desired delta echo time.
+    adc
+        ADC event object.
+    gx
+        Readout gradient object.
+    gx_pre
+        Pre-winder gradient object.
+    gx_post
+        Re-winder gradient object.
+    gx_between
+        Gradient between echoes.
+    """
+
+    def __init__(
+        self,
+        system: pp.Opts | None = None,
+        delta_te: float | None = None,
+        fov: float = 0.256,
+        n_readout: int = 128,
+        readout_oversampling: float = 2.0,
+        partial_echo_factor: float = 0.7,
+        gx_flat_time: float = 2.0e-3,
+        gx_pre_duration: float = 0.8e-3,
+    ):
+        """
+        Initialize the MultiEchoAcquisition class and compute all required attributes.
+
+        Parameters
+        ----------
+        system
+            PyPulseq system limits object.
+        delta_te
+            Desired echo spacing (in seconds). Minimum echo spacing is used if set to None.
+        fov
+            Field of view in x direction (in meters).
+        n_readout
+            Number of frequency encoding steps.
+        readout_oversampling
+            Readout oversampling factor.
+        partial_echo_factor
+            Partial echo factor.
+        gx_flat_time
+            Flat time of the readout gradient.
+        gx_pre_duration
+            Duration of readout pre-winder gradient.
+        """
+        # set system to default if not provided
+        self._system = sys_defaults if system is None else system
+
+        delta_k = 1 / (fov * readout_oversampling)
+        self._n_readout_post_echo = int(n_readout * readout_oversampling / 2 - 1)
+        self._n_readout_post_echo += np.mod(self._n_readout_post_echo + 1, 2)  # make odd
+        self._n_readout_pre_echo = int(
+            (n_readout * partial_echo_factor * readout_oversampling) - self._n_readout_post_echo - 1
+        )
+        self._n_readout_pre_echo += np.mod(self._n_readout_pre_echo, 2)  # make even
+
+        self._n_readout_with_partial_echo = self._n_readout_pre_echo + 1 + self._n_readout_post_echo
+        gx_flat_area = self._n_readout_with_partial_echo * delta_k
+
+        # adc dwell time has to be on adc raster and gx flat time on gradient raster
+        self._gx_flat_time, _ = find_gx_flat_time_on_adc_raster(
+            self._n_readout_with_partial_echo,
+            gx_flat_time / self._n_readout_with_partial_echo,
+            self._system.grad_raster_time,
+            self._system.adc_raster_time,
+        )
+
+        self._gx = pp.make_trapezoid(
+            channel='x', flat_area=gx_flat_area, flat_time=self._gx_flat_time, system=self._system
+        )
+
+        self._adc = pp.make_adc(
+            num_samples=self._n_readout_with_partial_echo,
+            duration=self._gx.flat_time,
+            delay=self._gx.rise_time,
+            system=self._system,
+        )
+
+        self._gx_pre = pp.make_trapezoid(
+            channel='x',
+            area=-(self._gx.amplitude * self._gx.rise_time / 2 + delta_k * (self._n_readout_pre_echo + 0.5)),
+            duration=gx_pre_duration * partial_echo_factor,
+            system=self._system,
+        )
+        self._gx_post = pp.make_trapezoid(
+            channel='x',
+            area=-(self._gx.amplitude * self._gx.fall_time / 2 + delta_k * (self._n_readout_post_echo + 0.5)),
+            duration=gx_pre_duration,
+            system=self._system,
+        )
+
+        self._gx_between = pp.make_trapezoid(
+            channel='x',
+            area=self._gx_pre.area - self._gx_post.area,
+            duration=gx_pre_duration,
+            system=self._system,
+        )
+
+        min_delta_te = pp.calc_duration(self._gx) + pp.calc_duration(self._gx_between)
+        if delta_te is None:
+            self._te_delay = 0.0
+        else:
+            self._te_delay = round_to_raster(delta_te - min_delta_te, self._system.block_duration_raster)
+            if not self._te_delay >= 0:
+                raise ValueError(
+                    f'Delta TE must be larger than {min_delta_te * 1000:.2f} ms. '
+                    f'Current value is {delta_te * 1000:.2f} ms.'
+                )
+
+    def add_to_seq(self, seq: pp.Sequence, n_echoes: int) -> tuple[pp.Sequence, list[float]]:
+        """Add all gradients and adc to sequence.
+
+        Parameters
+        ----------
+        seq
+            PyPulseq Sequence object.
+        n_echoes
+            Number of echoes
+
+        Returns
+        -------
+        seq
+            PyPulseq Sequence object.
+        time_to_echoes
+            Time from beginning of sequence to echoes.
+        """
+        # readout pre-winder
+        seq.add_block(self._gx_pre)
+
+        # add readout gradients and ADCs
+        seq, time_to_echoes = self.add_to_seq_without_pre_post_gradient(seq, n_echoes)
+
+        # readout re-winder
+        seq.add_block(self._gx_post)
+
+        return seq, time_to_echoes
+
+    def add_to_seq_without_pre_post_gradient(self, seq: pp.Sequence, n_echoes: int) -> tuple[pp.Sequence, list[float]]:
+        """Add readout gradients without pre- and re-winder gradients.
+
+        Often the pre- and re-winder gradients are played out at the same time as phase encoding gradients or spoiler
+        gradients.
+
+        Parameters
+        ----------
+        seq
+            PyPulseq Sequence object.
+        n_echoes
+            Number of echoes
+
+        Returns
+        -------
+        seq
+            PyPulseq Sequence object.
+        time_to_echoes
+            Time from beginning of sequence to echoes.
+        """
+        # add readout gradient and ADC
+        time_to_echoes = []
+        for echo_ in range(n_echoes):
+            start_of_current_gx = sum(seq.block_durations.values())
+            gx_sign = (-1) ** echo_
+            labels = []
+            labels.append(pp.make_label(type='SET', label='REV', value=gx_sign == -1))
+            labels.append(pp.make_label(label='REV', type='SET', value=gx_sign == -1))
+            labels.append(pp.make_label(label='ECO', type='SET', value=echo_))
+            seq.add_block(pp.scale_grad(self._gx, gx_sign), self._adc, *labels)
+            time_to_echoes.append(
+                start_of_current_gx + self._adc.delay + self._n_readout_pre_echo * self._adc.dwell + self._adc.dwell / 2
+            )
+            start_of_current_gx = sum(seq.block_durations.values())
+            if echo_ < n_echoes - 1:
+                if self._te_delay > 0:
+                    seq.add_block(pp.make_delay(self._te_delay))
+                seq.add_block(pp.scale_grad(self._gx_between, -gx_sign))
+
+        return seq, time_to_echoes
diff --git a/src/mrseq/utils/__init__.py b/src/mrseq/utils/__init__.py
index 00d413e..25e483b 100644
--- a/src/mrseq/utils/__init__.py
+++ b/src/mrseq/utils/__init__.py
@@ -1,5 +1,7 @@
 from mrseq.utils.sequence_helper import find_gx_flat_time_on_adc_raster, round_to_raster, write_sequence
 from mrseq.utils.system_defaults import sys_defaults
 from mrseq.utils.vds import variable_density_spiral_trajectory
-from mrseq.utils.trajectory import spiral_acquisition
+from mrseq.utils.spiral_sampling import spiral_acquisition
+from mrseq.utils.cartesian_sampling import cartesian_phase_encoding
+from mrseq.utils.MultiEchoAcquisition import MultiEchoAcquisition
 from mrseq.utils.ismrmrd import create_header, combine_ismrmrd_files
diff --git a/src/mrseq/utils/cartesian_sampling.py b/src/mrseq/utils/cartesian_sampling.py
new file mode 100644
index 0000000..e457452
--- /dev/null
+++ b/src/mrseq/utils/cartesian_sampling.py
@@ -0,0 +1,82 @@
+"""Cartesian trajectory calculation."""
+
+import warnings
+from typing import Literal
+
+import numpy as np
+
+
+def cartesian_phase_encoding(
+    n_phase_encoding: int,
+    acceleration: int = 1,
+    n_fully_sampled_center: int = 0,
+    sampling_order: Literal['linear', 'low_high', 'high_low', 'random'] = 'linear',
+    n_phase_encoding_per_shot: int | None = None,
+) -> tuple[np.ndarray, np.ndarray]:
+    """Calculate Cartesian sampling trajectory.
+
+    Parameters
+    ----------
+    n_phase_encoding
+        number of phase encoding points before undersampling
+    acceleration
+        undersampling factor
+    n_fully_sampled_center
+        number of phsae encoding points in the fully sampled center. This will reduce the overall undersampling factor.
+    sampling_order
+        order how phase encoding points are sampled
+    n_phase_encoding_per_shot
+        used to ensure that all phase encoding points can be acquired in an integer number of shots. If None, this
+        parameter is ignored, i.e. equal to n_phase_encoding_per_shot = 1
+    """
+    if n_fully_sampled_center > n_phase_encoding:
+        warnings.warn(
+            'Number of phase encoding steps in the fully sampled center will be reduced to the total number of phase '
+            + 'encoding steps.',
+            stacklevel=2,
+        )
+        n_fully_sampled_center = n_phase_encoding
+
+    if sampling_order == 'random':
+        # Linear order of a fully sampled kpe dimension. Undersampling is done later.
+        kpe = np.arange(0, n_phase_encoding)
+    else:
+        # Always include k-space center and more points on the negative side of k-space
+        kpe_pos = np.arange(0, n_phase_encoding // 2, acceleration)
+        kpe_neg = -np.arange(acceleration, n_phase_encoding // 2 + 1, acceleration)
+        kpe = np.concatenate((kpe_neg, kpe_pos), axis=0)
+
+    # Ensure fully sampled center
+    kpe_fully_sampled_center = np.arange(
+        -n_fully_sampled_center // 2, -n_fully_sampled_center // 2 + n_fully_sampled_center
+    )
+    kpe = np.unique(np.concatenate((kpe, kpe_fully_sampled_center)))
+
+    # Always acquire more to ensure desired resolution
+    if n_phase_encoding_per_shot and sampling_order != 'random':
+        kpe_extended = np.arange(-n_phase_encoding, n_phase_encoding)
+        kpe_extended = kpe_extended[np.argsort(np.abs(kpe_extended), kind='stable')]
+        idx = 0
+        while np.mod(len(kpe), n_phase_encoding_per_shot) > 0:
+            kpe = np.unique(np.concatenate((kpe, (kpe_extended[idx],))))
+            idx += 1
+
+    # Different temporal orders of phase encoding points
+    if sampling_order == 'random':
+        perm = np.random.permutation(kpe)
+        npe = len(perm) // acceleration
+        if n_phase_encoding_per_shot:
+            npe += n_phase_encoding_per_shot - np.mod(npe, n_phase_encoding_per_shot)
+        kpe = kpe[perm[:npe]]
+    elif sampling_order == 'linear':
+        kpe = np.sort(kpe)
+    elif sampling_order == 'low_high':
+        sort_idx = np.argsort(np.abs(kpe), kind='stable')
+        kpe = kpe[sort_idx]
+    elif sampling_order == 'high_low':
+        sort_idx = np.argsort(-np.abs(kpe), kind='stable')
+        kpe = kpe[sort_idx]
+    else:
+        raise ValueError(f'sampling order {sampling_order} not supported.')
+
+    return kpe, kpe_fully_sampled_center
diff --git a/src/mrseq/utils/trajectory.py b/src/mrseq/utils/spiral_sampling.py
similarity index 100%
rename from src/mrseq/utils/trajectory.py
rename to src/mrseq/utils/spiral_sampling.py
diff --git a/tests/utils/test_cartesian_sampling.py b/tests/utils/test_cartesian_sampling.py
new file mode 100644
index 0000000..64c3d3b
--- /dev/null
+++ b/tests/utils/test_cartesian_sampling.py
@@ -0,0 +1,67 @@
+"""Tests for Cartesian sampling."""
+
+from typing import Literal
+
+import numpy as np
+import pytest
+from mrseq.utils.cartesian_sampling import cartesian_phase_encoding
+
+
+@pytest.mark.parametrize('n_phase_encoding', [50, 51, 100])
+@pytest.mark.parametrize('acceleration', [1, 2, 3, 4, 6])
+@pytest.mark.parametrize('n_fully_sampled_center', [0, 8, 9])
+def test_cartesian_phase_encoding_identical_points(
+    n_phase_encoding: int, acceleration: int, n_fully_sampled_center: int
+):
+    """Test that linear, low-high and high-low cover same phase encoding points."""
+    pe_linear, pe_center_linear = cartesian_phase_encoding(
+        n_phase_encoding, acceleration, n_fully_sampled_center, sampling_order='linear'
+    )
+    pe_low_high, pe_center_low_high = cartesian_phase_encoding(
+        n_phase_encoding, acceleration, n_fully_sampled_center, sampling_order='low_high'
+    )
+    pe_high_low, pe_center_high_low = cartesian_phase_encoding(
+        n_phase_encoding, acceleration, n_fully_sampled_center, sampling_order='high_low'
+    )
+
+    np.testing.assert_allclose(pe_linear, np.sort(pe_low_high))
+    np.testing.assert_allclose(pe_linear, np.sort(pe_high_low))
+    np.testing.assert_allclose(pe_center_linear, np.sort(pe_center_low_high))
+    np.testing.assert_allclose(pe_center_linear, np.sort(pe_center_high_low))
+
+
+@pytest.mark.parametrize('pattern', ['linear', 'low_high', 'high_low', 'random'])
+def test_cartesian_phase_encoding_acceleration(pattern: Literal['linear', 'low_high', 'high_low', 'random']):
+    """Test correct undersampling factor."""
+    n_pe_full = 100
+    acceleration = 4
+
+    pe, _ = cartesian_phase_encoding(n_phase_encoding=n_pe_full, acceleration=acceleration, sampling_order=pattern)
+    assert len(pe) == n_pe_full // acceleration
+
+
+@pytest.mark.parametrize('pattern', ['linear', 'low_high', 'high_low', 'random'])
+@pytest.mark.parametrize('n_phase_encoding_per_shot', [3, 8, 11, 13])
+def test_cartesian_phase_encoding_integer_shots(
+    pattern: Literal['linear', 'low_high', 'high_low', 'random'],
+    n_phase_encoding_per_shot: int,
+):
+    """Test that the total number of phase encoding points lead to an integer number."""
+    n_pe_full = 100
+    acceleration = 4
+
+    pe, _ = cartesian_phase_encoding(
+        n_phase_encoding=n_pe_full,
+        acceleration=acceleration,
+        sampling_order=pattern,
+        n_phase_encoding_per_shot=n_phase_encoding_per_shot,
+    )
+    assert np.mod(len(pe), n_phase_encoding_per_shot) == 0
+
+
+def test_cartesian_phase_encoding_warning_fully_sampled_center():
+    """Test if warning is raised for a fully sampled center which is too large."""
+    with pytest.raises(Warning, match='Number of phase encoding steps in the fully sampled center will be reduced'):
+        cartesian_phase_encoding(
+            n_phase_encoding=10, acceleration=1, sampling_order='linear', n_fully_sampled_center=12
+        )
diff --git a/tests/utils/test_multi_echo_acquisition.py b/tests/utils/test_multi_echo_acquisition.py
new file mode 100644
index 0000000..97fb48a
--- /dev/null
+++ b/tests/utils/test_multi_echo_acquisition.py
@@ -0,0 +1,87 @@
+"""Tests for MultiEchoAcquisition."""
+
+import numpy as np
+import pypulseq as pp
+import pytest
+from mrseq.utils import MultiEchoAcquisition
+from scipy.signal import argrelextrema
+
+
+def test_multi_gradient_echo(system_defaults):
+    """Test multi-echo gradient echo readout as part of a simple sequence."""
+    seq = pp.Sequence(system=system_defaults)
+    rf = pp.make_block_pulse(
+        flip_angle=np.pi,
+        delay=system_defaults.rf_dead_time,
+        duration=2e-3,
+        phase_offset=0.0,
+        system=system_defaults,
+    )
+    seq.add_block(rf)
+    mecho = MultiEchoAcquisition(system=seq.system)
+    seq, _ = mecho.add_to_seq(seq, n_echoes=3)
+
+
+@pytest.mark.parametrize('delta_te', [3e-3, 5.34e-3])
+def test_multi_gradient_echo_set_delta_te(delta_te, system_defaults):
+    """Test pre-defined delta te."""
+    seq = pp.Sequence(system=system_defaults)
+    mecho = MultiEchoAcquisition(system=seq.system, delta_te=delta_te)
+    seq, time_to_echoes = mecho.add_to_seq(seq, 6)
+    np.testing.assert_allclose(np.diff(time_to_echoes), delta_te)
+
+
+def test_multi_gradient_echo_error_on_short_delta_te(system_defaults):
+    """Test if error is raised on too short delta echo time."""
+    with pytest.raises(ValueError):
+        MultiEchoAcquisition(system=system_defaults, delta_te=1e-6)
+
+
+@pytest.mark.parametrize('n_echoes', [1, 3, 8])
+@pytest.mark.parametrize('readout_oversampling', [1, 1.5, 2])
+@pytest.mark.parametrize('n_readout', [64, 128, 200])
+@pytest.mark.parametrize('partial_echo_factor', [1.0, 0.8, 0.7])
+def test_multi_gradient_echo_timing(n_echoes, readout_oversampling, n_readout, partial_echo_factor, system_defaults):
+    """Test that zero crossing of gradient moment coincides with echo time and correct adc sample."""
+    seq = pp.Sequence(system=system_defaults)
+    mecho = MultiEchoAcquisition(
+        system=seq.system,
+        n_readout=n_readout,
+        readout_oversampling=readout_oversampling,
+        partial_echo_factor=partial_echo_factor,
+    )
+    seq, time_to_echoes = mecho.add_to_seq(seq, n_echoes)
+    if n_echoes > 1:
+        # Ensure that the delta TE is the same between all echoes
+        assert len(np.unique(np.round(np.diff(time_to_echoes), decimals=6))) == 1
+
+    # Get full waveform for readout gradient
+    w = seq.waveforms_and_times()
+    gx_waveform = w[0][0][1]
+    gx_waveform_time = w[0][0][0]
+
+    # Find k0-crossings
+    max_grad = np.max(np.abs(gx_waveform))
+    dt = np.arange(gx_waveform_time[0], gx_waveform_time[-1], step=mecho._adc.dwell / 10)
+    gx_waveform_intp = np.interp(dt, gx_waveform_time, gx_waveform / max_grad)
+    m0_intp = np.cumsum(gx_waveform_intp) / len(gx_waveform_intp)
+    k0_idx = argrelextrema(np.abs(m0_intp), np.less, order=100)[0]
+
+    # Remove k0-crossings at the beginning and end of the block
+    k0_idx = np.array([ki for ki in k0_idx if (ki > 100 and ki < len(dt) - 100)])
+
+    # Zero-crossing of the readout gradient should be within +/- .5 adc dwell time of the k-space center sample which is
+    # the (_n_readout_pre_echo + 1)th sample. This should also be the same as the time_to_echo - time
+    assert n_echoes == len(k0_idx)
+    current_time = pp.calc_duration(mecho._gx_pre)
+    for echo in range(n_echoes):
+        time_of_k0_adc_sample = (
+            current_time + mecho._adc.delay + mecho._n_readout_pre_echo * mecho._adc.dwell + mecho._adc.dwell / 2
+        )
+        print(dt[k0_idx[echo]], time_of_k0_adc_sample, mecho._adc.dwell)
+        assert np.isclose(dt[k0_idx[echo]], time_of_k0_adc_sample, atol=mecho._adc.dwell / 2)
+        assert np.isclose(dt[k0_idx[echo]], time_to_echoes[echo], atol=mecho._adc.dwell / 2)
+
+        current_time += pp.calc_duration(mecho._gx) + pp.calc_duration(mecho._gx_between)
+
+    assert seq is not None
diff --git a/tests/utils/test_spiral_sampling.py b/tests/utils/test_spiral_sampling.py
new file mode 100644
index 0000000..26b3463
--- /dev/null
+++ b/tests/utils/test_spiral_sampling.py
@@ -0,0 +1,138 @@
+"""Tests for spiral sampling."""
+
+from typing import Literal
+
+import numpy as np
+import pypulseq as pp
+import pytest
+from mrseq.utils import spiral_acquisition
+from mrseq.utils.spiral_sampling import undersampled_variable_density_spiral
+
+
+def get_interp_waveform_for_gx_gy(seq: pp.Sequence, dt: np.ndarray | None = None, scale: float = 1.0):
+    """Interpolate gradient waveforms for the x and y axes.
+
+    Parameters
+    ----------
+    seq
+        The PyPulseq sequence object containing gradient waveforms.
+    dt
+        Desired time points for interpolation. If None, a default time array is generated.
+    scale
+        Scaling factor for the gradient waveforms. Default is 1.
+
+    Returns
+    -------
+    gx_waveform_intp
+        Interpolated gradient waveform for the x-axis.
+    gy_waveform_intp
+        Interpolated gradient waveform for the y-axis.
+    dt
+        Time points corresponding to the interpolated waveforms.
+    """
+    w = seq.waveforms_and_times()
+    gx_waveform = w[0][0][1] * scale
+    gx_waveform_time = w[0][0][0]
+
+    gy_waveform = w[0][1][1] * scale
+    gy_waveform_time = w[0][1][0]
+
+    if dt is None:
+        dt = np.arange(
+            min(gx_waveform_time[0], gy_waveform_time[0]), max(gx_waveform_time[-1], gy_waveform_time[-1]), step=1e-7
+        )
+    gx_waveform_intp = np.interp(dt, gx_waveform_time, gx_waveform)
+    gy_waveform_intp = np.interp(dt, gy_waveform_time, gy_waveform)
+
+    return gx_waveform_intp, gy_waveform_intp, dt
+
+
+@pytest.mark.parametrize('n_readout', (128, 256))
+@pytest.mark.parametrize('fov', (128e-3, 320e-3))
+@pytest.mark.parametrize('undersampling_factor', (1, 2, 3, 4))
+def test_undersampled_variable_density_spiral(
+    system_defaults: pp.Opts, n_readout: int, fov: float, undersampling_factor: float
+):
+    """Test spiral for different undersampling factors."""
+    traj, _grad, _s, _timing, _r, _theta, n_spirals, _fov_scaling_center, _fov_scaling_edge = (
+        undersampled_variable_density_spiral(system_defaults, n_readout, fov, undersampling_factor)
+    )
+    total_number_of_points = len(traj) * n_spirals
+    assert np.round(n_readout**2 / total_number_of_points) == undersampling_factor
+
+
+@pytest.mark.parametrize('n_readout', (64, 256))
+@pytest.mark.parametrize('fov', (128e-3, 320e-3))
+@pytest.mark.parametrize('n_spirals', (14, None))
+@pytest.mark.parametrize('undersampling_factor', (1, 3))
+@pytest.mark.parametrize('readout_oversampling', (1, 2, 4))
+@pytest.mark.parametrize('spiral_type', ('out', 'in-out'))
+def test_spiral_acquisition(
+    system_defaults: pp.Opts,
+    n_readout: int,
+    fov: float,
+    undersampling_factor: float,
+    n_spirals: int,
+    readout_oversampling: Literal[1, 2, 4],
+    spiral_type: Literal['out', 'in-out'],
+):
+    """Test spiral trajectories for different parameter combinations."""
+    g_pre_duration = 2e-3  # make this duration long to work for all combinations
+    system_defaults.adc_dead_time = 100e-6  # make this longer to ensure it impacts the timing
+
+    gx, gy, adc, trajectory, time_to_echo = spiral_acquisition(
+        system_defaults,
+        n_readout,
+        fov,
+        undersampling_factor,
+        readout_oversampling,
+        n_spirals,
+        g_pre_duration,
+        spiral_type=spiral_type,
+    )
+
+    # Verify timing for each spiral arm
+    for spiral_idx in range(len(gx)):
+        seq = pp.Sequence(system=system_defaults)
+        seq.add_block(gx[spiral_idx], gy[spiral_idx], adc)
+
+        # Get full waveform for readout gradient
+        gx_waveform_intp, gy_waveform_intp, dt = get_interp_waveform_for_gx_gy(seq)
+        max_grad = np.max(np.abs(gx_waveform_intp))
+        gx_waveform_intp /= max_grad
+        gy_waveform_intp /= max_grad
+
+        m0_intp = (np.abs(np.cumsum(gx_waveform_intp)) + np.abs(np.cumsum(gy_waveform_intp))) / (
+            2 * len(gx_waveform_intp)
+        )
+
+        if spiral_type == 'out':
+            k0_idx = np.argmin(m0_intp[:-100])
+        else:
+            k0_idx = np.argmin(m0_intp[100:-100]) + 100
+            assert m0_intp[0] < 1e-3
+        assert m0_intp[-1] < 1e-3
+        assert np.isclose(dt[k0_idx], time_to_echo, atol=system_defaults.grad_raster_time)
+
+        k_traj_adc = seq.calculate_kspace()[0]
+        # Ignore first and last elements because they are extrapolated for readout_oversampling > 1
+        k_traj_spiral = trajectory[spiral_idx, :, :]
+        if readout_oversampling > 1:
+            k_traj_adc = k_traj_adc[:, readout_oversampling // 2 : -readout_oversampling // 2]
+            k_traj_spiral = k_traj_spiral[readout_oversampling // 2 : -readout_oversampling // 2, :]
+        k_traj_adc /= np.max(np.abs(k_traj_adc))
+        k_traj_spiral /= np.max(np.abs(k_traj_spiral))
+        np.testing.assert_allclose(k_traj_adc[0, :], k_traj_spiral[:, 0], atol=2.5e-3)
+        np.testing.assert_allclose(k_traj_adc[1, :], k_traj_spiral[:, 1], atol=2.5e-3)
+
+    # Verify entire trajectory
+    seq = pp.Sequence(system=system_defaults)
+    for idx in range(len(gx)):
+        seq.add_block(gx[idx], gy[idx], adc)
+        seq.add_block(pp.make_delay(1e-3))
+
+    ok, error_report = seq.check_timing()
+    if not ok:
+        print('\nTiming check failed! Error listing follows\n')
+        print(error_report)
+    assert ok
diff --git a/tests/utils/test_trajectory.py b/tests/utils/test_trajectory.py
deleted file mode 100644
index 6a3cfdf..0000000
--- a/tests/utils/test_trajectory.py
+++ /dev/null
@@ -1,281 +0,0 @@
-"""Tests for sequence helper functions."""
-
-from typing import Literal
-
-import numpy as np
-import pypulseq as pp
-import pytest
-from mrseq.utils import spiral_acquisition
-from mrseq.utils.trajectory import MultiEchoAcquisition
-from mrseq.utils.trajectory import cartesian_phase_encoding
-from mrseq.utils.trajectory import undersampled_variable_density_spiral
-from scipy.signal import argrelextrema
-
-
-@pytest.mark.parametrize('n_phase_encoding', [50, 51, 100])
-@pytest.mark.parametrize('acceleration', [1, 2, 3, 4, 6])
-@pytest.mark.parametrize('n_fully_sampled_center', [0, 8, 9])
-def test_cartesian_phase_encoding_identical_points(
-    n_phase_encoding: int, acceleration: int, n_fully_sampled_center: int
-):
-    """Test that linear, low-high and high-low cover same phase encoding points."""
-    pe_linear, pe_center_linear = cartesian_phase_encoding(
-        n_phase_encoding, acceleration, n_fully_sampled_center, sampling_order='linear'
-    )
-    pe_low_high, pe_center_low_high = cartesian_phase_encoding(
-        n_phase_encoding, acceleration, n_fully_sampled_center, sampling_order='low_high'
-    )
-    pe_high_low, pe_center_high_low = cartesian_phase_encoding(
-        n_phase_encoding, acceleration, n_fully_sampled_center, sampling_order='high_low'
-    )
-
-    np.testing.assert_allclose(pe_linear, np.sort(pe_low_high))
-    np.testing.assert_allclose(pe_linear, np.sort(pe_high_low))
-    np.testing.assert_allclose(pe_center_linear, np.sort(pe_center_low_high))
-    np.testing.assert_allclose(pe_center_linear, np.sort(pe_center_high_low))
-
-
-@pytest.mark.parametrize('pattern', ['linear', 'low_high', 'high_low', 'random'])
-def test_cartesian_phase_encoding_acceleration(pattern: Literal['linear', 'low_high', 'high_low', 'random']):
-    """Test correct undersampling factor."""
-    n_pe_full = 100
-    acceleration = 4
-
-    pe, _ = cartesian_phase_encoding(n_phase_encoding=n_pe_full, acceleration=acceleration, sampling_order=pattern)
-    assert len(pe) == n_pe_full // acceleration
-
-
-@pytest.mark.parametrize('pattern', ['linear', 'low_high', 'high_low', 'random'])
-@pytest.mark.parametrize('n_phase_encoding_per_shot', [3, 8, 11, 13])
-def test_cartesian_phase_encoding_integer_shots(
-    pattern: Literal['linear', 'low_high', 'high_low', 'random'],
-    n_phase_encoding_per_shot: int,
-):
-    """Test that the total number of phase encoding points lead to an integer number."""
-    n_pe_full = 100
-    acceleration = 4
-
-    pe, _ = cartesian_phase_encoding(
-        n_phase_encoding=n_pe_full,
-        acceleration=acceleration,
-        sampling_order=pattern,
-        n_phase_encoding_per_shot=n_phase_encoding_per_shot,
-    )
-    assert np.mod(len(pe), n_phase_encoding_per_shot) == 0
-
-
-def test_cartesian_phase_encoding_warning_fully_sampled_center():
-    """Test if warning is raised for a fully sampled center which is too large."""
-    with pytest.raises(Warning, match='Number of phase encoding steps in the fully sampled center will be reduced'):
-        cartesian_phase_encoding(
-            n_phase_encoding=10, acceleration=1, sampling_order='linear', n_fully_sampled_center=12
-        )
-
-
-def test_multi_gradient_echo(system_defaults):
-    """Test multi-echo gradient echo readout as part of a simple sequence."""
-    seq = pp.Sequence(system=system_defaults)
-    rf = pp.make_block_pulse(
-        flip_angle=np.pi,
-        delay=system_defaults.rf_dead_time,
-        duration=2e-3,
-        phase_offset=0.0,
-        system=system_defaults,
-    )
-    seq.add_block(rf)
-    mecho = MultiEchoAcquisition(system=seq.system)
-    seq, _ = mecho.add_to_seq(seq, n_echoes=3)
-
-
-def get_interp_waveform_for_gx_gy(seq: pp.Sequence, dt: np.ndarray | None = None, scale: float = 1.0):
-    """Interpolate gradient waveforms for the x and y axes.
-
-    Parameters
-    ----------
-    seq
-        The PyPulseq sequence object containing gradient waveforms.
-    dt
-        Desired time points for interpolation. If None, a default time array is generated.
-    scale
-        Scaling factor for the gradient waveforms. Default is 1.
-
-    Returns
-    -------
-    gx_waveform_intp
-        Interpolated gradient waveform for the x-axis.
-    gy_waveform_intp
-        Interpolated gradient waveform for the y-axis.
-    dt
-        Time points corresponding to the interpolated waveforms.
-    """
-    w = seq.waveforms_and_times()
-    gx_waveform = w[0][0][1] * scale
-    gx_waveform_time = w[0][0][0]
-
-    gy_waveform = w[0][1][1] * scale
-    gy_waveform_time = w[0][1][0]
-
-    if dt is None:
-        dt = np.arange(
-            min(gx_waveform_time[0], gy_waveform_time[0]), max(gx_waveform_time[-1], gy_waveform_time[-1]), step=1e-7
-        )
-    gx_waveform_intp = np.interp(dt, gx_waveform_time, gx_waveform)
-    gy_waveform_intp = np.interp(dt, gy_waveform_time, gy_waveform)
-
-    return gx_waveform_intp, gy_waveform_intp, dt
-
-
-@pytest.mark.parametrize('n_readout', (128, 256))
-@pytest.mark.parametrize('fov', (128e-3, 320e-3))
-@pytest.mark.parametrize('undersampling_factor', (1, 2, 3, 4))
-def test_undersampled_variable_density_spiral(
-    system_defaults: pp.Opts, n_readout: int, fov: float, undersampling_factor: float
-):
-    """Test spiral for different undersampling factors."""
-    traj, _grad, _s, _timing, _r, _theta, n_spirals, _fov_scaling_center, _fov_scaling_edge = (
-        undersampled_variable_density_spiral(system_defaults, n_readout, fov, undersampling_factor)
-    )
-    total_number_of_points = len(traj) * n_spirals
-    assert np.round(n_readout**2 / total_number_of_points) == undersampling_factor
-
-
-@pytest.mark.parametrize('n_readout', (64, 256))
-@pytest.mark.parametrize('fov', (128e-3, 320e-3))
-@pytest.mark.parametrize('n_spirals', (14, None))
-@pytest.mark.parametrize('undersampling_factor', (1, 3))
-@pytest.mark.parametrize('readout_oversampling', (1, 2, 4))
-@pytest.mark.parametrize('spiral_type', ('out', 'in-out'))
-def test_spiral_acquisition(
-    system_defaults: pp.Opts,
-    n_readout: int,
-    fov: float,
-    undersampling_factor: float,
-    n_spirals: int,
-    readout_oversampling: Literal[1, 2, 4],
-    spiral_type: Literal['out', 'in-out'],
-):
-    """Test spiral trajectories for different parameter combinations."""
-    g_pre_duration = 2e-3  # make this duration long to work for all combinations
-    system_defaults.adc_dead_time = 100e-6  # make this longer to ensure it impacts the timing
-
-    gx, gy, adc, trajectory, time_to_echo = spiral_acquisition(
-        system_defaults,
-        n_readout,
-        fov,
-        undersampling_factor,
-        readout_oversampling,
-        n_spirals,
-        g_pre_duration,
-        spiral_type=spiral_type,
-    )
-
-    # Verify timing for each spiral arm
-    for spiral_idx in range(len(gx)):
-        seq = pp.Sequence(system=system_defaults)
-        seq.add_block(gx[spiral_idx], gy[spiral_idx], adc)
-
-        # Get full waveform for readout gradient
-        gx_waveform_intp, gy_waveform_intp, dt = get_interp_waveform_for_gx_gy(seq)
-        max_grad = np.max(np.abs(gx_waveform_intp))
-        gx_waveform_intp /= max_grad
-        gy_waveform_intp /= max_grad
-
-        m0_intp = (np.abs(np.cumsum(gx_waveform_intp)) + np.abs(np.cumsum(gy_waveform_intp))) / (
-            2 * len(gx_waveform_intp)
-        )
-
-        if spiral_type == 'out':
-            k0_idx = np.argmin(m0_intp[:-100])
-        else:
-            k0_idx = np.argmin(m0_intp[100:-100]) + 100
-            assert m0_intp[0] < 1e-3
-        assert m0_intp[-1] < 1e-3
-        assert np.isclose(dt[k0_idx], time_to_echo, atol=system_defaults.grad_raster_time)
-
-        k_traj_adc = seq.calculate_kspace()[0]
-        # Ignore first and last elements because they are extrapolated for readout_oversampling > 1
-        k_traj_spiral = trajectory[spiral_idx, :, :]
-        if readout_oversampling > 1:
-            k_traj_adc = k_traj_adc[:, readout_oversampling // 2 : -readout_oversampling // 2]
-            k_traj_spiral = k_traj_spiral[readout_oversampling // 2 : -readout_oversampling // 2, :]
-        k_traj_adc /= np.max(np.abs(k_traj_adc))
-        k_traj_spiral /= np.max(np.abs(k_traj_spiral))
-        np.testing.assert_allclose(k_traj_adc[0, :], k_traj_spiral[:, 0], atol=2.5e-3)
-        np.testing.assert_allclose(k_traj_adc[1, :], k_traj_spiral[:, 1], atol=2.5e-3)
-
-    # Verify entire trajectory
-    seq = pp.Sequence(system=system_defaults)
-    for idx in range(len(gx)):
-        seq.add_block(gx[idx], gy[idx], adc)
-        seq.add_block(pp.make_delay(1e-3))
-
-    ok, error_report = seq.check_timing()
-    if not ok:
-        print('\nTiming check failed! Error listing follows\n')
-        print(error_report)
-    assert ok
-
-
-@pytest.mark.parametrize('delta_te', [3e-3, 5.34e-3])
-def test_multi_gradient_echo_set_delta_te(delta_te, system_defaults):
-    """Test pre-defined delta te."""
-    seq = pp.Sequence(system=system_defaults)
-    mecho = MultiEchoAcquisition(system=seq.system, delta_te=delta_te)
-    seq, time_to_echoes = mecho.add_to_seq(seq, 6)
-    np.testing.assert_allclose(np.diff(time_to_echoes), delta_te)
-
-
-def test_multi_gradient_echo_error_on_short_delta_te(system_defaults):
-    """Test if error is raised on too short delta echo time."""
-    with pytest.raises(ValueError):
-        MultiEchoAcquisition(system=system_defaults, delta_te=1e-6)
-
-
-@pytest.mark.parametrize('n_echoes', [1, 3, 8])
-@pytest.mark.parametrize('readout_oversampling', [1, 1.5, 2])
-@pytest.mark.parametrize('n_readout', [64, 128, 200])
-@pytest.mark.parametrize('partial_echo_factor', [1.0, 0.8, 0.7])
-def test_multi_gradient_echo_timing(n_echoes, readout_oversampling, n_readout, partial_echo_factor, system_defaults):
-    """Test that zero crossing of gradient moment coincides with echo time and correct adc sample."""
-    seq = pp.Sequence(system=system_defaults)
-    mecho = MultiEchoAcquisition(
-        system=seq.system,
-        n_readout=n_readout,
-        readout_oversampling=readout_oversampling,
-        partial_echo_factor=partial_echo_factor,
-    )
-    seq, time_to_echoes = mecho.add_to_seq(seq, n_echoes)
-    if n_echoes > 1:
-        # Ensure that the delta TE is the same between all echoes
-        assert len(np.unique(np.round(np.diff(time_to_echoes), decimals=6))) == 1
-
-    # Get full waveform for readout gradient
-    w = seq.waveforms_and_times()
-    gx_waveform = w[0][0][1]
-    gx_waveform_time = w[0][0][0]
-
-    # Find k0-crossings
-    max_grad = np.max(np.abs(gx_waveform))
-    dt = np.arange(gx_waveform_time[0], gx_waveform_time[-1], step=mecho._adc.dwell / 10)
-    gx_waveform_intp = np.interp(dt, gx_waveform_time, gx_waveform / max_grad)
-    m0_intp = np.cumsum(gx_waveform_intp) / len(gx_waveform_intp)
-    k0_idx = argrelextrema(np.abs(m0_intp), np.less, order=100)[0]
-
-    # Remove k0-crossings at the beginning and end of the block
-    k0_idx = np.array([ki for ki in k0_idx if (ki > 100 and ki < len(dt) - 100)])
-
-    # Zero-crossing of the readout gradient should be within +/- .5 adc dwell time of the k-space center sample which is
-    # the (_n_readout_pre_echo + 1)th sample. This should also be the same as the time_to_echo - time
-    assert n_echoes == len(k0_idx)
-    current_time = pp.calc_duration(mecho._gx_pre)
-    for echo in range(n_echoes):
-        time_of_k0_adc_sample = (
-            current_time + mecho._adc.delay + mecho._n_readout_pre_echo * mecho._adc.dwell + mecho._adc.dwell / 2
-        )
-        print(dt[k0_idx[echo]], time_of_k0_adc_sample, mecho._adc.dwell)
-        assert np.isclose(dt[k0_idx[echo]], time_of_k0_adc_sample, atol=mecho._adc.dwell / 2)
-        assert np.isclose(dt[k0_idx[echo]], time_to_echoes[echo], atol=mecho._adc.dwell / 2)
-
-        current_time += pp.calc_duration(mecho._gx) + pp.calc_duration(mecho._gx_between)
-
-    assert seq is not None

From 4710e91bb4431c6f9d4e28f88ebea18222b30d19 Mon Sep 17 00:00:00 2001
From: Christoph Kolbitsch <christoph.kolbitsch@ptb.de>
Date: Mon, 16 Mar 2026 20:45:06 +0000
Subject: [PATCH 2/6] add colab badge

---
 .github/dependabot.yml                      |   2 +-
 examples/radial_flash.ipynb                 |  51 ++--
 examples/spiral_flash.ipynb                 |  51 ++--
 examples/t1_inv_rec_gre_single_line.ipynb   |  53 ++--
 examples/t1_inv_rec_se_single_line.ipynb    |  53 ++--
 examples/t1_molli_bssfp.ipynb               |  57 ++--
 examples/t1_t2_spiral_cmrf.ipynb            |  53 ++--
 examples/t1rho_se_single_line.ipynb         |  53 ++--
 examples/t2_multi_echo_se_single_line.ipynb |  53 ++--
 examples/t2_t2prep_flash.ipynb              |  55 ++--
 examples/t2star_multi_echo_flash.ipynb      |  55 ++--
 src/mrseq/utils/spiral_sampling.py          | 275 --------------------
 12 files changed, 373 insertions(+), 438 deletions(-)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 11d0cb6..142397f 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -3,7 +3,7 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "daily"
+      interval: "monthly"
     groups:
       all-actions:
         patterns: ["*"]
diff --git a/examples/radial_flash.ipynb b/examples/radial_flash.ipynb
index 775364e..5c0883c 100644
--- a/examples/radial_flash.ipynb
+++ b/examples/radial_flash.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/radial_flash.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# Radial FLASH\n",
     "\n",
@@ -12,7 +20,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -21,7 +29,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -44,7 +65,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -55,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -69,7 +90,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -80,7 +101,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -90,7 +111,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the radial FLASH sequence\n",
@@ -101,7 +122,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -119,7 +140,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -130,7 +151,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,7 +163,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct the image\n",
@@ -152,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +184,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "### Compare to theoretical model\n",
@@ -174,7 +195,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -184,7 +205,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/spiral_flash.ipynb b/examples/spiral_flash.ipynb
index 77dbad9..936927c 100644
--- a/examples/spiral_flash.ipynb
+++ b/examples/spiral_flash.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/spiral_flash.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# Spiral FLASH\n",
     "\n",
@@ -12,7 +20,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -21,7 +29,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -44,7 +65,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -55,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -69,7 +90,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -80,7 +101,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -90,7 +111,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the spiral FLASH sequence\n",
@@ -101,7 +122,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -119,7 +140,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -130,7 +151,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,7 +163,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct the image\n",
@@ -152,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +184,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "### Compare to theoretical model\n",
@@ -174,7 +195,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -184,7 +205,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/t1_inv_rec_gre_single_line.ipynb b/examples/t1_inv_rec_gre_single_line.ipynb
index 4ce6734..35f345e 100644
--- a/examples/t1_inv_rec_gre_single_line.ipynb
+++ b/examples/t1_inv_rec_gre_single_line.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/t1_inv_rec_gre_single_line.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# T1 Mapping - IR GRE\n",
     "\n",
@@ -13,7 +21,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -22,7 +30,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -48,7 +69,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -58,7 +79,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +92,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -82,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,7 +113,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the IR-GRE sequence\n",
@@ -103,7 +124,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +141,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -131,7 +152,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,7 +163,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct the images at different inversion times\n",
@@ -153,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -166,7 +187,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "We can now plot the images at different inversion times."
@@ -175,7 +196,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -190,7 +211,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "### Estimate the T1 maps\n",
@@ -200,7 +221,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/t1_inv_rec_se_single_line.ipynb b/examples/t1_inv_rec_se_single_line.ipynb
index 3775785..c8565f3 100644
--- a/examples/t1_inv_rec_se_single_line.ipynb
+++ b/examples/t1_inv_rec_se_single_line.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/t1_inv_rec_se_single_line.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# T1 Mapping - IR SE\n",
     "\n",
@@ -13,7 +21,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -22,7 +30,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -48,7 +69,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -58,7 +79,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +92,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -82,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,7 +113,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the IR-SE sequence\n",
@@ -103,7 +124,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +141,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -130,7 +151,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +162,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct the images at different inversion times\n",
@@ -152,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -165,7 +186,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "We can now plot the images at different inversion times."
@@ -174,7 +195,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -189,7 +210,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "### Estimate the T1 maps\n",
@@ -199,7 +220,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/t1_molli_bssfp.ipynb b/examples/t1_molli_bssfp.ipynb
index b4631fd..28b56ab 100644
--- a/examples/t1_molli_bssfp.ipynb
+++ b/examples/t1_molli_bssfp.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/t1_molli_bssfp.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# T1 Mapping - MOLLI\n",
     "\n",
@@ -13,7 +21,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -22,7 +30,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -51,7 +72,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -61,7 +82,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -73,7 +94,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -84,7 +105,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -98,7 +119,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the MOLLI bSSFP sequence\n",
@@ -109,7 +130,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -125,7 +146,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -135,7 +156,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -146,7 +167,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct the images at different inversion times\n",
@@ -157,7 +178,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -178,7 +199,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "We visualize the coil sensitivity maps which we used for the iterative SENSE reconstruction."
@@ -187,7 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -198,7 +219,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "We can now plot the images at different inversion times."
@@ -207,7 +228,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -229,7 +250,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "17",
+   "id": "19",
    "metadata": {},
    "source": [
     "### Estimate the T1 maps\n",
@@ -239,7 +260,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/t1_t2_spiral_cmrf.ipynb b/examples/t1_t2_spiral_cmrf.ipynb
index b3dcaf6..7672b79 100644
--- a/examples/t1_t2_spiral_cmrf.ipynb
+++ b/examples/t1_t2_spiral_cmrf.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/t1_t2_spiral_cmrf.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# T1 and T2 Mapping - Spiral cMRF\n",
     "\n",
@@ -12,7 +20,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -21,7 +29,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -49,7 +70,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -61,7 +82,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +95,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -87,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -99,7 +120,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the spiral cardiac MRF sequence\n",
@@ -110,7 +131,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -127,7 +148,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -137,7 +158,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -149,7 +170,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct series of images showing the dynamic contrast change\n",
@@ -160,7 +181,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -182,7 +203,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "We can now plot the images at different time points along the acquisition."
@@ -191,7 +212,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -206,7 +227,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "### Estimate the T1 and T2 maps\n",
@@ -216,7 +237,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/t1rho_se_single_line.ipynb b/examples/t1rho_se_single_line.ipynb
index 72e4644..b5a2b0b 100644
--- a/examples/t1rho_se_single_line.ipynb
+++ b/examples/t1rho_se_single_line.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/t1rho_se_single_line.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# T1rho Mapping\n",
     "\n",
@@ -13,7 +21,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -22,7 +30,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -48,7 +69,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -58,7 +79,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -70,7 +91,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -81,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,7 +113,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the Spin-lock SE sequence\n",
@@ -103,7 +124,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -119,7 +140,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -129,7 +150,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -140,7 +161,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct the images at different spin-lock times\n",
@@ -150,7 +171,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +184,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "We can now plot the images at different inversion times."
@@ -172,7 +193,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -188,7 +209,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "### Estimate the T1rho maps\n",
@@ -199,7 +220,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/t2_multi_echo_se_single_line.ipynb b/examples/t2_multi_echo_se_single_line.ipynb
index 3d5b44a..3deb39e 100644
--- a/examples/t2_multi_echo_se_single_line.ipynb
+++ b/examples/t2_multi_echo_se_single_line.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/t2_multi_echo_se_single_line.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# T2 Mapping - Multi-echo SE\n",
     "\n",
@@ -13,7 +21,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -22,7 +30,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -48,7 +69,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -58,7 +79,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +92,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -82,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,7 +113,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the multi-echo SE sequence\n",
@@ -103,7 +124,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +141,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -130,7 +151,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +162,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct the images at different echo times\n",
@@ -152,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -165,7 +186,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "We can now plot the images at different inversion times."
@@ -174,7 +195,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -189,7 +210,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "### Estimate the T2 maps\n",
@@ -199,7 +220,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/t2_t2prep_flash.ipynb b/examples/t2_t2prep_flash.ipynb
index e27cc64..b719cef 100644
--- a/examples/t2_t2prep_flash.ipynb
+++ b/examples/t2_t2prep_flash.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/t2_t2prep_flash.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# T2 Mapping - T2prep FLASH\n",
     "\n",
@@ -12,7 +20,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -21,7 +29,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,7 +68,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -57,7 +78,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -70,7 +91,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -82,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +116,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the T2prep FLASH sequence\n",
@@ -105,7 +126,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "source": [
     "For in-vivo applications we have to make sure the sequence can be run within a breathhold. This would require undersampling (acceleration > 1) and obtaining a high number of phase encoding points in each cardiac cycle. This will impair the accuracy of the obtained T2 maps. For the evaluation here we can make the sequence longer to increase accuracy.  "
@@ -114,7 +135,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -133,7 +154,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -143,7 +164,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -154,7 +175,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "source": [
     "### Reconstruct the images with different T2-preparation pulses.\n",
@@ -165,7 +186,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -178,7 +199,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "source": [
     "We can now plot the images with different T2-preparation times."
@@ -187,7 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -202,7 +223,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "source": [
     "### Estimate the T2 maps\n",
@@ -212,7 +233,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/examples/t2star_multi_echo_flash.ipynb b/examples/t2star_multi_echo_flash.ipynb
index f41e875..46d1046 100644
--- a/examples/t2star_multi_echo_flash.ipynb
+++ b/examples/t2star_multi_echo_flash.ipynb
@@ -4,6 +4,14 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/t2star_multi_echo_flash.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "# T2* Mapping - Multi-echo FLASH\n",
     "\n",
@@ -12,7 +20,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "source": [
     "### Imports"
@@ -21,7 +29,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import importlib\n",
+    "\n",
+    "if not importlib.util.find_spec('mrseq'):\n",
+    "    %pip install mrseq[examples]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -51,7 +72,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Settings\n",
@@ -62,7 +83,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +95,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "7",
    "metadata": {},
    "source": [
     "### Create the digital phantom\n",
@@ -85,7 +106,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +121,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "source": [
     "### Create the $T2^*$ mapping sequence\n",
@@ -111,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -129,7 +150,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Simulate the sequence\n",
@@ -140,7 +161,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -152,7 +173,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
     "### Reconstruct the image\n",
@@ -162,7 +183,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -180,7 +201,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "We can now visualize the images obtained at the different echo times."
@@ -189,7 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -204,7 +225,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "source": [
     "### Estimate $T2^*$\n",
@@ -215,7 +236,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,7 +246,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/src/mrseq/utils/spiral_sampling.py b/src/mrseq/utils/spiral_sampling.py
index 91beacd..584858e 100644
--- a/src/mrseq/utils/spiral_sampling.py
+++ b/src/mrseq/utils/spiral_sampling.py
@@ -1,289 +1,14 @@
 """Basic functionality for trajectory calculation."""
 
-import warnings
 from typing import Any
 from typing import Literal
 
 import numpy as np
 import pypulseq as pp
 
-from mrseq.utils import find_gx_flat_time_on_adc_raster
-from mrseq.utils import round_to_raster
-from mrseq.utils import sys_defaults
 from mrseq.utils import variable_density_spiral_trajectory
 
 
-def cartesian_phase_encoding(
-    n_phase_encoding: int,
-    acceleration: int = 1,
-    n_fully_sampled_center: int = 0,
-    sampling_order: Literal['linear', 'low_high', 'high_low', 'random'] = 'linear',
-    n_phase_encoding_per_shot: int | None = None,
-) -> tuple[np.ndarray, np.ndarray]:
-    """Calculate Cartesian sampling trajectory.
-
-    Parameters
-    ----------
-    n_phase_encoding
-        number of phase encoding points before undersampling
-    acceleration
-        undersampling factor
-    n_fully_sampled_center
-        number of phsae encoding points in the fully sampled center. This will reduce the overall undersampling factor.
-    sampling_order
-        order how phase encoding points are sampled
-    n_phase_encoding_per_shot
-        used to ensure that all phase encoding points can be acquired in an integer number of shots. If None, this
-        parameter is ignored, i.e. equal to n_phase_encoding_per_shot = 1
-    """
-    if n_fully_sampled_center > n_phase_encoding:
-        warnings.warn(
-            'Number of phase encoding steps in the fully sampled center will be reduced to the total number of phase '
-            + 'encoding steps.',
-            stacklevel=2,
-        )
-        n_fully_sampled_center = n_phase_encoding
-
-    if sampling_order == 'random':
-        # Linear order of a fully sampled kpe dimension. Undersampling is done later.
-        kpe = np.arange(0, n_phase_encoding)
-    else:
-        # Always include k-space center and more points on the negative side of k-space
-        kpe_pos = np.arange(0, n_phase_encoding // 2, acceleration)
-        kpe_neg = -np.arange(acceleration, n_phase_encoding // 2 + 1, acceleration)
-        kpe = np.concatenate((kpe_neg, kpe_pos), axis=0)
-
-    # Ensure fully sampled center
-    kpe_fully_sampled_center = np.arange(
-        -n_fully_sampled_center // 2, -n_fully_sampled_center // 2 + n_fully_sampled_center
-    )
-    kpe = np.unique(np.concatenate((kpe, kpe_fully_sampled_center)))
-
-    # Always acquire more to ensure desired resolution
-    if n_phase_encoding_per_shot and sampling_order != 'random':
-        kpe_extended = np.arange(-n_phase_encoding, n_phase_encoding)
-        kpe_extended = kpe_extended[np.argsort(np.abs(kpe_extended), kind='stable')]
-        idx = 0
-        while np.mod(len(kpe), n_phase_encoding_per_shot) > 0:
-            kpe = np.unique(np.concatenate((kpe, (kpe_extended[idx],))))
-            idx += 1
-
-    # Different temporal orders of phase encoding points
-    if sampling_order == 'random':
-        perm = np.random.permutation(kpe)
-        npe = len(perm) // acceleration
-        if n_phase_encoding_per_shot:
-            npe += n_phase_encoding_per_shot - np.mod(npe, n_phase_encoding_per_shot)
-        kpe = kpe[perm[:npe]]
-    elif sampling_order == 'linear':
-        kpe = np.sort(kpe)
-    elif sampling_order == 'low_high':
-        sort_idx = np.argsort(np.abs(kpe), kind='stable')
-        kpe = kpe[sort_idx]
-    elif sampling_order == 'high_low':
-        sort_idx = np.argsort(-np.abs(kpe), kind='stable')
-        kpe = kpe[sort_idx]
-    else:
-        raise ValueError(f'sampling order {sampling_order} not supported.')
-
-    return kpe, kpe_fully_sampled_center
-
-
-class MultiEchoAcquisition:
-    """
-    Multi-echo gradient echo acquisition.
-
-    Attributes
-    ----------
-    system
-        PyPulseq system limits object.
-    n_readout_post_echo
-        Number of readout points after echo.
-    n_readout_pre_echo
-        Number of readout points before echo.
-    n_readout_with_partial_echo
-        Total number of readout points with partial echo.
-    te_delay
-        Additional delay after readout gradient gx to achieve desired delta echo time.
-    adc
-        ADC event object.
-    gx
-        Readout gradient object.
-    gx_pre
-        Pre-winder gradient object.
-    gx_post
-        Re-winder gradient object.
-    gx_between
-        Gradient between echoes.
-    """
-
-    def __init__(
-        self,
-        system: pp.Opts | None = None,
-        delta_te: float | None = None,
-        fov: float = 0.256,
-        n_readout: int = 128,
-        readout_oversampling: float = 2.0,
-        partial_echo_factor: float = 0.7,
-        gx_flat_time: float = 2.0e-3,
-        gx_pre_duration: float = 0.8e-3,
-    ):
-        """
-        Initialize the MultiEchoAcquisition class and compute all required attributes.
-
-        Parameters
-        ----------
-        system
-            PyPulseq system limits object.
-        delta_te
-            Desired echo spacing (in seconds). Minimum echo spacing is used if set to None.
-        fov
-            Field of view in x direction (in meters).
-        n_readout
-            Number of frequency encoding steps.
-        readout_oversampling
-            Readout oversampling factor.
-        partial_echo_factor
-            Partial echo factor.
-        gx_flat_time
-            Flat time of the readout gradient.
-        gx_pre_duration
-            Duration of readout pre-winder gradient.
-        """
-        # set system to default if not provided
-        self._system = sys_defaults if system is None else system
-
-        delta_k = 1 / (fov * readout_oversampling)
-        self._n_readout_post_echo = int(n_readout * readout_oversampling / 2 - 1)
-        self._n_readout_post_echo += np.mod(self._n_readout_post_echo + 1, 2)  # make odd
-        self._n_readout_pre_echo = int(
-            (n_readout * partial_echo_factor * readout_oversampling) - self._n_readout_post_echo - 1
-        )
-        self._n_readout_pre_echo += np.mod(self._n_readout_pre_echo, 2)  # make even
-
-        self._n_readout_with_partial_echo = self._n_readout_pre_echo + 1 + self._n_readout_post_echo
-        gx_flat_area = self._n_readout_with_partial_echo * delta_k
-
-        # adc dwell time has to be on adc raster and gx flat time on gradient raster
-        self._gx_flat_time, _ = find_gx_flat_time_on_adc_raster(
-            self._n_readout_with_partial_echo,
-            gx_flat_time / self._n_readout_with_partial_echo,
-            self._system.grad_raster_time,
-            self._system.adc_raster_time,
-        )
-
-        self._gx = pp.make_trapezoid(
-            channel='x', flat_area=gx_flat_area, flat_time=self._gx_flat_time, system=self._system
-        )
-
-        self._adc = pp.make_adc(
-            num_samples=self._n_readout_with_partial_echo,
-            duration=self._gx.flat_time,
-            delay=self._gx.rise_time,
-            system=self._system,
-        )
-
-        self._gx_pre = pp.make_trapezoid(
-            channel='x',
-            area=-(self._gx.amplitude * self._gx.rise_time / 2 + delta_k * (self._n_readout_pre_echo + 0.5)),
-            duration=gx_pre_duration * partial_echo_factor,
-            system=self._system,
-        )
-        self._gx_post = pp.make_trapezoid(
-            channel='x',
-            area=-(self._gx.amplitude * self._gx.fall_time / 2 + delta_k * (self._n_readout_post_echo + 0.5)),
-            duration=gx_pre_duration,
-            system=self._system,
-        )
-
-        self._gx_between = pp.make_trapezoid(
-            channel='x',
-            area=self._gx_pre.area - self._gx_post.area,
-            duration=gx_pre_duration,
-            system=self._system,
-        )
-
-        min_delta_te = pp.calc_duration(self._gx) + pp.calc_duration(self._gx_between)
-        if delta_te is None:
-            self._te_delay = 0.0
-        else:
-            self._te_delay = round_to_raster(delta_te - min_delta_te, self._system.block_duration_raster)
-            if not self._te_delay >= 0:
-                raise ValueError(
-                    f'Delta TE must be larger than {min_delta_te * 1000:.2f} ms. '
-                    f'Current value is {delta_te * 1000:.2f} ms.'
-                )
-
-    def add_to_seq(self, seq: pp.Sequence, n_echoes: int) -> tuple[pp.Sequence, list[float]]:
-        """Add all gradients and adc to sequence.
-
-        Parameters
-        ----------
-        seq
-            PyPulseq Sequence object.
-        n_echoes
-            Number of echoes
-
-        Returns
-        -------
-        seq
-            PyPulseq Sequence object.
-        time_to_echoes
-            Time from beginning of sequence to echoes.
-        """
-        # readout pre-winder
-        seq.add_block(self._gx_pre)
-
-        # add readout gradients and ADCs
-        seq, time_to_echoes = self.add_to_seq_without_pre_post_gradient(seq, n_echoes)
-
-        # readout re-winder
-        seq.add_block(self._gx_post)
-
-        return seq, time_to_echoes
-
-    def add_to_seq_without_pre_post_gradient(self, seq: pp.Sequence, n_echoes: int) -> tuple[pp.Sequence, list[float]]:
-        """Add readout gradients without pre- and re-winder gradients.
-
-        Often the pre- and re-winder gradients are played out at the same time as phase encoding gradients or spoiler
-        gradients.
-
-        Parameters
-        ----------
-        seq
-            PyPulseq Sequence object.
-        n_echoes
-            Number of echoes
-
-        Returns
-        -------
-        seq
-            PyPulseq Sequence object.
-        time_to_echoes
-            Time from beginning of sequence to echoes.
-        """
-        # add readout gradient and ADC
-        time_to_echoes = []
-        for echo_ in range(n_echoes):
-            start_of_current_gx = sum(seq.block_durations.values())
-            gx_sign = (-1) ** echo_
-            labels = []
-            labels.append(pp.make_label(type='SET', label='REV', value=gx_sign == -1))
-            labels.append(pp.make_label(label='REV', type='SET', value=gx_sign == -1))
-            labels.append(pp.make_label(label='ECO', type='SET', value=echo_))
-            seq.add_block(pp.scale_grad(self._gx, gx_sign), self._adc, *labels)
-            time_to_echoes.append(
-                start_of_current_gx + self._adc.delay + self._n_readout_pre_echo * self._adc.dwell + self._adc.dwell / 2
-            )
-            start_of_current_gx = sum(seq.block_durations.values())
-            if echo_ < n_echoes - 1:
-                if self._te_delay > 0:
-                    seq.add_block(pp.make_delay(self._te_delay))
-                seq.add_block(pp.scale_grad(self._gx_between, -gx_sign))
-
-        return seq, time_to_echoes
-
-
 def undersampled_variable_density_spiral(
     system: pp.Opts, n_readout: int, fov: float, undersampling_factor: float
 ) -> tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray, int, float, float]:

From 02c3c8ecb91835d9514f8104fca2eb6b190cff9c Mon Sep 17 00:00:00 2001
From: Christoph Kolbitsch <christoph.kolbitsch@ptb.de>
Date: Mon, 16 Mar 2026 20:53:23 +0000
Subject: [PATCH 3/6] reduce example install

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index dc236f9..20c6f7a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,8 +54,8 @@ tests = [
     "pytest-cov",
     "pytest-xdist",
 ]
-examples = ["mrzerocore>=0.4.3", "mrpro", "cmap", "jupyter-book<2.0"]
-dev = ["mrseq[tests, examples]"]
+examples = ["mrzerocore>=0.4.3", "mrpro", "cmap"]
+dev = ["mrseq[tests, examples]", "jupyter-book<2.0"]
 
 [project.urls]
 "repository" = "https://github.com/PTB-MR/mrseq"

From 18acedbce9a01d35a4e14e7309dfc73585fffcb1 Mon Sep 17 00:00:00 2001
From: Christoph Kolbitsch <christoph.kolbitsch@ptb.de>
Date: Mon, 16 Mar 2026 20:57:21 +0000
Subject: [PATCH 4/6] install dev for building example documentation

---
 .github/workflows/examples.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
index 9efafdf..cd6a2fd 100644
--- a/.github/workflows/examples.yml
+++ b/.github/workflows/examples.yml
@@ -25,7 +25,7 @@ jobs:
         run: |
           pip install --index-url=https://download.pytorch.org/whl/cpu \
                       --extra-index-url https://pypi.org/simple/ \
-                      --upgrade --upgrade-strategy eager -e .[examples]
+                      --upgrade --upgrade-strategy eager -e .[dev]
 
       # Build the book
       - name: Build the book

From 444d6ff99e5ffd9c2834272eeb399f31297bf772 Mon Sep 17 00:00:00 2001
From: Christoph Kolbitsch <christoph.kolbitsch@ptb.de>
Date: Tue, 17 Mar 2026 13:59:42 +0000
Subject: [PATCH 5/6] rename sequences

---
 examples/grpe_flash_dixon.ipynb                                 | 2 +-
 examples/radial_flash.ipynb                                     | 2 +-
 examples/spiral_flash.ipynb                                     | 2 +-
 examples/t1_inv_rec_gre_single_line.ipynb                       | 2 +-
 examples/t1_inv_rec_se_single_line.ipynb                        | 2 +-
 examples/t1_molli_bssfp.ipynb                                   | 2 +-
 examples/t1_t2_spiral_cmrf.ipynb                                | 2 +-
 examples/t1rho_se_single_line.ipynb                             | 2 +-
 examples/t2_multi_echo_se_single_line.ipynb                     | 2 +-
 examples/t2_t2prep_flash.ipynb                                  | 2 +-
 examples/t2star_multi_echo_flash.ipynb                          | 2 +-
 src/mrseq/{scripts => sequences}/__init__.py                    | 0
 src/mrseq/{scripts => sequences}/grpe_flash_dixon.py            | 0
 src/mrseq/{scripts => sequences}/radial_flash.py                | 0
 src/mrseq/{scripts => sequences}/spiral_flash.py                | 0
 src/mrseq/{scripts => sequences}/t1_inv_rec_gre_single_line.py  | 0
 src/mrseq/{scripts => sequences}/t1_inv_rec_se_single_line.py   | 0
 src/mrseq/{scripts => sequences}/t1_molli_bssfp.py              | 0
 src/mrseq/{scripts => sequences}/t1_t2_spiral_cmrf.py           | 0
 src/mrseq/{scripts => sequences}/t1rho_se_single_line.py        | 0
 .../{scripts => sequences}/t2_multi_echo_se_single_line.py      | 0
 src/mrseq/{scripts => sequences}/t2_t2prep_flash.py             | 0
 src/mrseq/{scripts => sequences}/t2star_multi_echo_flash.py     | 0
 tests/{scripts => sequences}/__init__.py                        | 0
 tests/{scripts => sequences}/test_grpe_flash_dixon.py           | 2 +-
 tests/{scripts => sequences}/test_radial_flash.py               | 2 +-
 tests/{scripts => sequences}/test_spiral_flash.py               | 2 +-
 tests/{scripts => sequences}/test_t1_inv_rec_gre_single_line.py | 2 +-
 tests/{scripts => sequences}/test_t1_inv_rec_se_single_line.py  | 2 +-
 tests/{scripts => sequences}/test_t1_molli_bssfp.py             | 2 +-
 tests/{scripts => sequences}/test_t1_t2_spiral_cmrf.py          | 2 +-
 tests/{scripts => sequences}/test_t1rho_se_single_line.py       | 2 +-
 .../{scripts => sequences}/test_t2_multi_echo_se_single_line.py | 2 +-
 tests/{scripts => sequences}/test_t2_t2prep_flash.py            | 2 +-
 tests/{scripts => sequences}/test_t2star_multi_echo_flash.py    | 2 +-
 35 files changed, 22 insertions(+), 22 deletions(-)
 rename src/mrseq/{scripts => sequences}/__init__.py (100%)
 rename src/mrseq/{scripts => sequences}/grpe_flash_dixon.py (100%)
 rename src/mrseq/{scripts => sequences}/radial_flash.py (100%)
 rename src/mrseq/{scripts => sequences}/spiral_flash.py (100%)
 rename src/mrseq/{scripts => sequences}/t1_inv_rec_gre_single_line.py (100%)
 rename src/mrseq/{scripts => sequences}/t1_inv_rec_se_single_line.py (100%)
 rename src/mrseq/{scripts => sequences}/t1_molli_bssfp.py (100%)
 rename src/mrseq/{scripts => sequences}/t1_t2_spiral_cmrf.py (100%)
 rename src/mrseq/{scripts => sequences}/t1rho_se_single_line.py (100%)
 rename src/mrseq/{scripts => sequences}/t2_multi_echo_se_single_line.py (100%)
 rename src/mrseq/{scripts => sequences}/t2_t2prep_flash.py (100%)
 rename src/mrseq/{scripts => sequences}/t2star_multi_echo_flash.py (100%)
 rename tests/{scripts => sequences}/__init__.py (100%)
 rename tests/{scripts => sequences}/test_grpe_flash_dixon.py (96%)
 rename tests/{scripts => sequences}/test_radial_flash.py (96%)
 rename tests/{scripts => sequences}/test_spiral_flash.py (96%)
 rename tests/{scripts => sequences}/test_t1_inv_rec_gre_single_line.py (94%)
 rename tests/{scripts => sequences}/test_t1_inv_rec_se_single_line.py (94%)
 rename tests/{scripts => sequences}/test_t1_molli_bssfp.py (93%)
 rename tests/{scripts => sequences}/test_t1_t2_spiral_cmrf.py (90%)
 rename tests/{scripts => sequences}/test_t1rho_se_single_line.py (95%)
 rename tests/{scripts => sequences}/test_t2_multi_echo_se_single_line.py (94%)
 rename tests/{scripts => sequences}/test_t2_t2prep_flash.py (95%)
 rename tests/{scripts => sequences}/test_t2star_multi_echo_flash.py (94%)

diff --git a/examples/grpe_flash_dixon.ipynb b/examples/grpe_flash_dixon.ipynb
index 6a49333..41abbb7 100644
--- a/examples/grpe_flash_dixon.ipynb
+++ b/examples/grpe_flash_dixon.ipynb
@@ -45,7 +45,7 @@
     "from mrpro.operators.models import SpoiledGRE\n",
     "from scipy.interpolate import interp1d\n",
     "\n",
-    "from mrseq.scripts.grpe_flash_dixon import main as create_seq\n",
+    "from mrseq.sequences.grpe_flash_dixon import main as create_seq\n",
     "from mrseq.utils import combine_ismrmrd_files\n",
     "from mrseq.utils import sys_defaults"
    ]
diff --git a/examples/radial_flash.ipynb b/examples/radial_flash.ipynb
index 33e7712..2912767 100644
--- a/examples/radial_flash.ipynb
+++ b/examples/radial_flash.ipynb
@@ -58,7 +58,7 @@
     "from mrpro.data.traj_calculators import KTrajectoryIsmrmrd\n",
     "from mrpro.operators.models import SpoiledGRE\n",
     "\n",
-    "from mrseq.scripts.radial_flash import main as create_seq\n",
+    "from mrseq.sequences.radial_flash import main as create_seq\n",
     "from mrseq.utils import combine_ismrmrd_files\n",
     "from mrseq.utils import sys_defaults"
    ]
diff --git a/examples/spiral_flash.ipynb b/examples/spiral_flash.ipynb
index 936927c..b7edade 100644
--- a/examples/spiral_flash.ipynb
+++ b/examples/spiral_flash.ipynb
@@ -58,7 +58,7 @@
     "from mrpro.data.traj_calculators import KTrajectoryIsmrmrd\n",
     "from mrpro.operators.models import SpoiledGRE\n",
     "\n",
-    "from mrseq.scripts.spiral_flash import main as create_seq\n",
+    "from mrseq.sequences.spiral_flash import main as create_seq\n",
     "from mrseq.utils import combine_ismrmrd_files\n",
     "from mrseq.utils import sys_defaults"
    ]
diff --git a/examples/t1_inv_rec_gre_single_line.ipynb b/examples/t1_inv_rec_gre_single_line.ipynb
index 35f345e..f1a4d67 100644
--- a/examples/t1_inv_rec_gre_single_line.ipynb
+++ b/examples/t1_inv_rec_gre_single_line.ipynb
@@ -63,7 +63,7 @@
     "from mrpro.operators import DictionaryMatchOp\n",
     "from mrpro.operators.models import InversionRecovery\n",
     "\n",
-    "from mrseq.scripts.t1_inv_rec_gre_single_line import main as create_seq\n",
+    "from mrseq.sequences.t1_inv_rec_gre_single_line import main as create_seq\n",
     "from mrseq.utils import sys_defaults"
    ]
   },
diff --git a/examples/t1_inv_rec_se_single_line.ipynb b/examples/t1_inv_rec_se_single_line.ipynb
index c8565f3..fffac79 100644
--- a/examples/t1_inv_rec_se_single_line.ipynb
+++ b/examples/t1_inv_rec_se_single_line.ipynb
@@ -63,7 +63,7 @@
     "from mrpro.operators import DictionaryMatchOp\n",
     "from mrpro.operators.models import InversionRecovery\n",
     "\n",
-    "from mrseq.scripts.t1_inv_rec_se_single_line import main as create_seq\n",
+    "from mrseq.sequences.t1_inv_rec_se_single_line import main as create_seq\n",
     "from mrseq.utils import sys_defaults"
    ]
   },
diff --git a/examples/t1_molli_bssfp.ipynb b/examples/t1_molli_bssfp.ipynb
index cb1e1b2..219f064 100644
--- a/examples/t1_molli_bssfp.ipynb
+++ b/examples/t1_molli_bssfp.ipynb
@@ -66,7 +66,7 @@
     "from mrpro.operators.models import MOLLI\n",
     "from mrpro.phantoms.coils import birdcage_2d\n",
     "\n",
-    "from mrseq.scripts.t1_molli_bssfp import main as create_seq\n",
+    "from mrseq.sequences.t1_molli_bssfp import main as create_seq\n",
     "from mrseq.utils import sys_defaults"
    ]
   },
diff --git a/examples/t1_t2_spiral_cmrf.ipynb b/examples/t1_t2_spiral_cmrf.ipynb
index 7672b79..4be7412 100644
--- a/examples/t1_t2_spiral_cmrf.ipynb
+++ b/examples/t1_t2_spiral_cmrf.ipynb
@@ -63,7 +63,7 @@
     "from mrpro.operators import DictionaryMatchOp\n",
     "from mrpro.operators.models import CardiacFingerprinting\n",
     "\n",
-    "from mrseq.scripts.t1_t2_spiral_cmrf import main as create_seq\n",
+    "from mrseq.sequences.t1_t2_spiral_cmrf import main as create_seq\n",
     "from mrseq.utils import combine_ismrmrd_files\n",
     "from mrseq.utils import sys_defaults"
    ]
diff --git a/examples/t1rho_se_single_line.ipynb b/examples/t1rho_se_single_line.ipynb
index b5a2b0b..77faaa0 100644
--- a/examples/t1rho_se_single_line.ipynb
+++ b/examples/t1rho_se_single_line.ipynb
@@ -63,7 +63,7 @@
     "from mrpro.operators import DictionaryMatchOp\n",
     "from mrpro.operators.models import MonoExponentialDecay\n",
     "\n",
-    "from mrseq.scripts.t1rho_se_single_line import main as create_seq\n",
+    "from mrseq.sequences.t1rho_se_single_line import main as create_seq\n",
     "from mrseq.utils import sys_defaults"
    ]
   },
diff --git a/examples/t2_multi_echo_se_single_line.ipynb b/examples/t2_multi_echo_se_single_line.ipynb
index 3deb39e..98a1e37 100644
--- a/examples/t2_multi_echo_se_single_line.ipynb
+++ b/examples/t2_multi_echo_se_single_line.ipynb
@@ -63,7 +63,7 @@
     "from mrpro.operators import DictionaryMatchOp\n",
     "from mrpro.operators.models import MonoExponentialDecay\n",
     "\n",
-    "from mrseq.scripts.t2_multi_echo_se_single_line import main as create_seq\n",
+    "from mrseq.sequences.t2_multi_echo_se_single_line import main as create_seq\n",
     "from mrseq.utils import sys_defaults"
    ]
   },
diff --git a/examples/t2_t2prep_flash.ipynb b/examples/t2_t2prep_flash.ipynb
index b719cef..9d0dcc0 100644
--- a/examples/t2_t2prep_flash.ipynb
+++ b/examples/t2_t2prep_flash.ipynb
@@ -62,7 +62,7 @@
     "from mrpro.operators import DictionaryMatchOp\n",
     "from mrpro.operators.models import MonoExponentialDecay\n",
     "\n",
-    "from mrseq.scripts.t2_t2prep_flash import main as create_seq\n",
+    "from mrseq.sequences.t2_t2prep_flash import main as create_seq\n",
     "from mrseq.utils import sys_defaults"
    ]
   },
diff --git a/examples/t2star_multi_echo_flash.ipynb b/examples/t2star_multi_echo_flash.ipynb
index 46d1046..09d33b7 100644
--- a/examples/t2star_multi_echo_flash.ipynb
+++ b/examples/t2star_multi_echo_flash.ipynb
@@ -65,7 +65,7 @@
     "from mrpro.operators.models import MonoExponentialDecay\n",
     "from mrpro.phantoms.coils import birdcage_2d\n",
     "\n",
-    "from mrseq.scripts.t2star_multi_echo_flash import main as create_seq\n",
+    "from mrseq.sequences.t2star_multi_echo_flash import main as create_seq\n",
     "from mrseq.utils import combine_ismrmrd_files\n",
     "from mrseq.utils import sys_defaults"
    ]
diff --git a/src/mrseq/scripts/__init__.py b/src/mrseq/sequences/__init__.py
similarity index 100%
rename from src/mrseq/scripts/__init__.py
rename to src/mrseq/sequences/__init__.py
diff --git a/src/mrseq/scripts/grpe_flash_dixon.py b/src/mrseq/sequences/grpe_flash_dixon.py
similarity index 100%
rename from src/mrseq/scripts/grpe_flash_dixon.py
rename to src/mrseq/sequences/grpe_flash_dixon.py
diff --git a/src/mrseq/scripts/radial_flash.py b/src/mrseq/sequences/radial_flash.py
similarity index 100%
rename from src/mrseq/scripts/radial_flash.py
rename to src/mrseq/sequences/radial_flash.py
diff --git a/src/mrseq/scripts/spiral_flash.py b/src/mrseq/sequences/spiral_flash.py
similarity index 100%
rename from src/mrseq/scripts/spiral_flash.py
rename to src/mrseq/sequences/spiral_flash.py
diff --git a/src/mrseq/scripts/t1_inv_rec_gre_single_line.py b/src/mrseq/sequences/t1_inv_rec_gre_single_line.py
similarity index 100%
rename from src/mrseq/scripts/t1_inv_rec_gre_single_line.py
rename to src/mrseq/sequences/t1_inv_rec_gre_single_line.py
diff --git a/src/mrseq/scripts/t1_inv_rec_se_single_line.py b/src/mrseq/sequences/t1_inv_rec_se_single_line.py
similarity index 100%
rename from src/mrseq/scripts/t1_inv_rec_se_single_line.py
rename to src/mrseq/sequences/t1_inv_rec_se_single_line.py
diff --git a/src/mrseq/scripts/t1_molli_bssfp.py b/src/mrseq/sequences/t1_molli_bssfp.py
similarity index 100%
rename from src/mrseq/scripts/t1_molli_bssfp.py
rename to src/mrseq/sequences/t1_molli_bssfp.py
diff --git a/src/mrseq/scripts/t1_t2_spiral_cmrf.py b/src/mrseq/sequences/t1_t2_spiral_cmrf.py
similarity index 100%
rename from src/mrseq/scripts/t1_t2_spiral_cmrf.py
rename to src/mrseq/sequences/t1_t2_spiral_cmrf.py
diff --git a/src/mrseq/scripts/t1rho_se_single_line.py b/src/mrseq/sequences/t1rho_se_single_line.py
similarity index 100%
rename from src/mrseq/scripts/t1rho_se_single_line.py
rename to src/mrseq/sequences/t1rho_se_single_line.py
diff --git a/src/mrseq/scripts/t2_multi_echo_se_single_line.py b/src/mrseq/sequences/t2_multi_echo_se_single_line.py
similarity index 100%
rename from src/mrseq/scripts/t2_multi_echo_se_single_line.py
rename to src/mrseq/sequences/t2_multi_echo_se_single_line.py
diff --git a/src/mrseq/scripts/t2_t2prep_flash.py b/src/mrseq/sequences/t2_t2prep_flash.py
similarity index 100%
rename from src/mrseq/scripts/t2_t2prep_flash.py
rename to src/mrseq/sequences/t2_t2prep_flash.py
diff --git a/src/mrseq/scripts/t2star_multi_echo_flash.py b/src/mrseq/sequences/t2star_multi_echo_flash.py
similarity index 100%
rename from src/mrseq/scripts/t2star_multi_echo_flash.py
rename to src/mrseq/sequences/t2star_multi_echo_flash.py
diff --git a/tests/scripts/__init__.py b/tests/sequences/__init__.py
similarity index 100%
rename from tests/scripts/__init__.py
rename to tests/sequences/__init__.py
diff --git a/tests/scripts/test_grpe_flash_dixon.py b/tests/sequences/test_grpe_flash_dixon.py
similarity index 96%
rename from tests/scripts/test_grpe_flash_dixon.py
rename to tests/sequences/test_grpe_flash_dixon.py
index 34759eb..0dce989 100644
--- a/tests/scripts/test_grpe_flash_dixon.py
+++ b/tests/sequences/test_grpe_flash_dixon.py
@@ -1,7 +1,7 @@
 """Tests for 3D FLASH sequence with golden radial phase encoding."""
 
 import pytest
-from mrseq.scripts.grpe_flash_dixon import main as create_seq
+from mrseq.sequences.grpe_flash_dixon import main as create_seq
 
 EXPECTED_DUR = 17.84831  # defined 2025-11-09
 
diff --git a/tests/scripts/test_radial_flash.py b/tests/sequences/test_radial_flash.py
similarity index 96%
rename from tests/scripts/test_radial_flash.py
rename to tests/sequences/test_radial_flash.py
index 8d031c3..2616d3c 100644
--- a/tests/scripts/test_radial_flash.py
+++ b/tests/sequences/test_radial_flash.py
@@ -2,7 +2,7 @@
 
 import numpy as np
 import pytest
-from mrseq.scripts.radial_flash import main as create_seq
+from mrseq.sequences.radial_flash import main as create_seq
 
 EXPECTED_DUR = 0.75043  # defined 2025-10-17
 
diff --git a/tests/scripts/test_spiral_flash.py b/tests/sequences/test_spiral_flash.py
similarity index 96%
rename from tests/scripts/test_spiral_flash.py
rename to tests/sequences/test_spiral_flash.py
index 42983b2..5a55e69 100644
--- a/tests/scripts/test_spiral_flash.py
+++ b/tests/sequences/test_spiral_flash.py
@@ -2,7 +2,7 @@
 
 import numpy as np
 import pytest
-from mrseq.scripts.spiral_flash import main as create_seq
+from mrseq.sequences.spiral_flash import main as create_seq
 
 EXPECTED_DUR = 0.70588  # defined 2026-02-10
 
diff --git a/tests/scripts/test_t1_inv_rec_gre_single_line.py b/tests/sequences/test_t1_inv_rec_gre_single_line.py
similarity index 94%
rename from tests/scripts/test_t1_inv_rec_gre_single_line.py
rename to tests/sequences/test_t1_inv_rec_gre_single_line.py
index 26685c0..a4e2d5c 100644
--- a/tests/scripts/test_t1_inv_rec_gre_single_line.py
+++ b/tests/sequences/test_t1_inv_rec_gre_single_line.py
@@ -1,7 +1,7 @@
 """Tests for Gold standard GRE-based inversion recovery sequence."""
 
 import pytest
-from mrseq.scripts.t1_inv_rec_gre_single_line import main as create_seq
+from mrseq.sequences.t1_inv_rec_gre_single_line import main as create_seq
 
 EXPECTED_DUR = 7168.000320  # defined 2025-02-03
 
diff --git a/tests/scripts/test_t1_inv_rec_se_single_line.py b/tests/sequences/test_t1_inv_rec_se_single_line.py
similarity index 94%
rename from tests/scripts/test_t1_inv_rec_se_single_line.py
rename to tests/sequences/test_t1_inv_rec_se_single_line.py
index 5b628c4..4f7a5cc 100644
--- a/tests/scripts/test_t1_inv_rec_se_single_line.py
+++ b/tests/sequences/test_t1_inv_rec_se_single_line.py
@@ -1,7 +1,7 @@
 """Tests for Gold standard SE-based inversion recovery sequence."""
 
 import pytest
-from mrseq.scripts.t1_inv_rec_se_single_line import main as create_seq
+from mrseq.sequences.t1_inv_rec_se_single_line import main as create_seq
 
 EXPECTED_DUR = 7168.000320  # defined 2025-02-03
 
diff --git a/tests/scripts/test_t1_molli_bssfp.py b/tests/sequences/test_t1_molli_bssfp.py
similarity index 93%
rename from tests/scripts/test_t1_molli_bssfp.py
rename to tests/sequences/test_t1_molli_bssfp.py
index 0c084de..9de7b25 100644
--- a/tests/scripts/test_t1_molli_bssfp.py
+++ b/tests/sequences/test_t1_molli_bssfp.py
@@ -1,7 +1,7 @@
 """Tests for 2D Cartesian FLASH with T2-preparation pulses for T2 mapping."""
 
 import pytest
-from mrseq.scripts.t1_molli_bssfp import main as create_seq
+from mrseq.sequences.t1_molli_bssfp import main as create_seq
 
 EXPECTED_DUR = 10.95339  # defined 2025-11-24
 
diff --git a/tests/scripts/test_t1_t2_spiral_cmrf.py b/tests/sequences/test_t1_t2_spiral_cmrf.py
similarity index 90%
rename from tests/scripts/test_t1_t2_spiral_cmrf.py
rename to tests/sequences/test_t1_t2_spiral_cmrf.py
index b210ed3..be7f6ea 100644
--- a/tests/scripts/test_t1_t2_spiral_cmrf.py
+++ b/tests/sequences/test_t1_t2_spiral_cmrf.py
@@ -1,7 +1,7 @@
 """Tests for cardiac MR Fingerprinting sequence with spiral readout."""
 
 import pytest
-from mrseq.scripts.t1_t2_spiral_cmrf import main as create_seq
+from mrseq.sequences.t1_t2_spiral_cmrf import main as create_seq
 
 EXPECTED_DUR = 14.55141  # defined 2026-02-10
 
diff --git a/tests/scripts/test_t1rho_se_single_line.py b/tests/sequences/test_t1rho_se_single_line.py
similarity index 95%
rename from tests/scripts/test_t1rho_se_single_line.py
rename to tests/sequences/test_t1rho_se_single_line.py
index 30b9662..161c37b 100644
--- a/tests/scripts/test_t1rho_se_single_line.py
+++ b/tests/sequences/test_t1rho_se_single_line.py
@@ -1,7 +1,7 @@
 """Tests for Gold standard SE-based T1rho mapping sequence."""
 
 import pytest
-from mrseq.scripts.t1rho_se_single_line import main as create_seq
+from mrseq.sequences.t1rho_se_single_line import main as create_seq
 
 EXPECTED_DUR = 3072.000000  # defined 2025-02-20
 
diff --git a/tests/scripts/test_t2_multi_echo_se_single_line.py b/tests/sequences/test_t2_multi_echo_se_single_line.py
similarity index 94%
rename from tests/scripts/test_t2_multi_echo_se_single_line.py
rename to tests/sequences/test_t2_multi_echo_se_single_line.py
index 2967f33..ed4312f 100644
--- a/tests/scripts/test_t2_multi_echo_se_single_line.py
+++ b/tests/sequences/test_t2_multi_echo_se_single_line.py
@@ -2,7 +2,7 @@
 
 import numpy as np
 import pytest
-from mrseq.scripts.t2_multi_echo_se_single_line import main as create_seq
+from mrseq.sequences.t2_multi_echo_se_single_line import main as create_seq
 
 EXPECTED_DUR = 5120.000970  # defined 2025-02-06
 
diff --git a/tests/scripts/test_t2_t2prep_flash.py b/tests/sequences/test_t2_t2prep_flash.py
similarity index 95%
rename from tests/scripts/test_t2_t2prep_flash.py
rename to tests/sequences/test_t2_t2prep_flash.py
index d0f356c..dca3aa3 100644
--- a/tests/scripts/test_t2_t2prep_flash.py
+++ b/tests/sequences/test_t2_t2prep_flash.py
@@ -2,7 +2,7 @@
 
 import numpy as np
 import pytest
-from mrseq.scripts.t2_t2prep_flash import main as create_seq
+from mrseq.sequences.t2_t2prep_flash import main as create_seq
 
 EXPECTED_DUR = 8.17667  # defined 2026-01-26
 
diff --git a/tests/scripts/test_t2star_multi_echo_flash.py b/tests/sequences/test_t2star_multi_echo_flash.py
similarity index 94%
rename from tests/scripts/test_t2star_multi_echo_flash.py
rename to tests/sequences/test_t2star_multi_echo_flash.py
index c428cd7..436a0d1 100644
--- a/tests/scripts/test_t2star_multi_echo_flash.py
+++ b/tests/sequences/test_t2star_multi_echo_flash.py
@@ -1,7 +1,7 @@
 """Tests for 2D Cartesian FLASH with T2-preparation pulses for T2 mapping."""
 
 import pytest
-from mrseq.scripts.t2star_multi_echo_flash import main as create_seq
+from mrseq.sequences.t2star_multi_echo_flash import main as create_seq
 
 EXPECTED_DUR = 2.83989  # defined 2025-11-22
 

From 784b5167311b1d61fe57266743833c05188edc9d Mon Sep 17 00:00:00 2001
From: Christoph Kolbitsch <christoph.kolbitsch@ptb.de>
Date: Mon, 23 Mar 2026 10:21:03 +0000
Subject: [PATCH 6/6] move set def to kernels

---
 src/mrseq/sequences/grpe_flash_dixon.py       | 19 +++++++-------
 src/mrseq/sequences/radial_flash.py           | 18 ++++++-------
 src/mrseq/sequences/spiral_flash.py           | 16 ++++++------
 .../sequences/t1_inv_rec_gre_single_line.py   | 18 ++++++-------
 .../sequences/t1_inv_rec_se_single_line.py    | 18 ++++++-------
 src/mrseq/sequences/t1_molli_bssfp.py         | 20 +++++++-------
 src/mrseq/sequences/t1_t2_spiral_cmrf.py      | 26 +++++++++----------
 src/mrseq/sequences/t1rho_se_single_line.py   | 18 ++++++-------
 .../sequences/t2_multi_echo_se_single_line.py | 14 +++++-----
 src/mrseq/sequences/t2_t2prep_flash.py        | 18 ++++++-------
 .../sequences/t2star_multi_echo_flash.py      | 19 +++++++-------
 11 files changed, 103 insertions(+), 101 deletions(-)

diff --git a/src/mrseq/sequences/grpe_flash_dixon.py b/src/mrseq/sequences/grpe_flash_dixon.py
index 2265a91..7b4d694 100644
--- a/src/mrseq/sequences/grpe_flash_dixon.py
+++ b/src/mrseq/sequences/grpe_flash_dixon.py
@@ -434,6 +434,15 @@ def grpe_flash_dixon_kernel(
         prot.close()
 
     delta_te_array = np.diff(time_to_echoes)
+
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_x, fov_y, fov_z])
+    seq.set_definition('ReconMatrix', (n_readout, n_rpe_points, n_rpe_points))
+    seq.set_definition('SliceThickness', fov_z)
+    seq.set_definition('TE', [(te or float(min_te)) + idx * float(delta_te_array[0]) for idx in range(n_echoes)])
+    seq.set_definition('TR', tr or float(min_tr))
+    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
+
     return seq, float(min_te), float(min_tr), float(delta_te_array[0])
 
 
@@ -537,7 +546,7 @@ def main(
     if (output_path / Path(filename + '_header.h5')).exists():
         (output_path / Path(filename + '_header.h5')).unlink()
 
-    seq, min_te, min_tr, delta_te = grpe_flash_dixon_kernel(
+    seq, _min_te, min_tr, delta_te = grpe_flash_dixon_kernel(
         system=system,
         te=te,
         delta_te=delta_te,
@@ -580,14 +589,6 @@ def main(
         print('\nCreating advanced test report...')
         print(seq.test_report())
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_x, fov_y, fov_z])
-    seq.set_definition('ReconMatrix', (n_readout, n_rpe_points, n_rpe_points))
-    seq.set_definition('SliceThickness', fov_z)
-    seq.set_definition('TE', [(te or min_te) + idx * delta_te for idx in range(n_echoes)])
-    seq.set_definition('TR', tr or min_tr)
-    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
-
     # save seq-file to disk
     print(f"\nSaving sequence file '{filename}.seq' into folder '{output_path}'.")
     write_sequence(seq, str(output_path / filename), create_signature=True, v141_compatibility=v141_compatibility)
diff --git a/src/mrseq/sequences/radial_flash.py b/src/mrseq/sequences/radial_flash.py
index 316100c..e590eb2 100644
--- a/src/mrseq/sequences/radial_flash.py
+++ b/src/mrseq/sequences/radial_flash.py
@@ -279,6 +279,14 @@ def radial_flash_kernel(
     if mrd_header_file:
         prot.close()
 
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness * n_slices])
+    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', te or min_te)
+    seq.set_definition('TR', tr or min_tr)
+    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
+
     return seq, min_te, min_tr
 
 
@@ -374,7 +382,7 @@ def main(
     if (output_path / Path(filename + '_header.h5')).exists():
         (output_path / Path(filename + '_header.h5')).unlink()
 
-    seq, min_te, min_tr = radial_flash_kernel(
+    seq, _min_te, min_tr = radial_flash_kernel(
         system=system,
         te=te,
         tr=tr,
@@ -412,14 +420,6 @@ def main(
         print('\nCreating advanced test report...')
         print(seq.test_report())
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness * n_slices])
-    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', te or min_te)
-    seq.set_definition('TR', tr or min_tr)
-    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
-
     # save seq-file to disk
     print(f"\nSaving sequence file '{filename}.seq' into folder '{output_path}'.")
     write_sequence(seq, str(output_path / filename), create_signature=True, v141_compatibility=v141_compatibility)
diff --git a/src/mrseq/sequences/spiral_flash.py b/src/mrseq/sequences/spiral_flash.py
index 8a03c9e..219adbd 100644
--- a/src/mrseq/sequences/spiral_flash.py
+++ b/src/mrseq/sequences/spiral_flash.py
@@ -247,6 +247,13 @@ def spiral_flash_kernel(
     if mrd_header_file:
         prot.close()
 
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness * n_slices])
+    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', te or min_te)
+    seq.set_definition('TR', tr or min_tr)
+
     return seq, min_te, min_tr
 
 
@@ -336,7 +343,7 @@ def main(
     if (output_path / Path(filename + '_header.h5')).exists():
         (output_path / Path(filename + '_header.h5')).unlink()
 
-    seq, min_te, min_tr = spiral_flash_kernel(
+    seq, _min_te, min_tr = spiral_flash_kernel(
         system=system,
         te=te,
         tr=tr,
@@ -372,13 +379,6 @@ def main(
         print('\nCreating advanced test report...')
         print(seq.test_report())
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness * n_slices])
-    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', te or min_te)
-    seq.set_definition('TR', tr or min_tr)
-
     # save seq-file to disk
     print(f"\nSaving sequence file '{filename}.seq' into folder '{output_path}'.")
     write_sequence(seq, str(output_path / filename), create_signature=True, v141_compatibility=v141_compatibility)
diff --git a/src/mrseq/sequences/t1_inv_rec_gre_single_line.py b/src/mrseq/sequences/t1_inv_rec_gre_single_line.py
index 19402b6..2c5187d 100644
--- a/src/mrseq/sequences/t1_inv_rec_gre_single_line.py
+++ b/src/mrseq/sequences/t1_inv_rec_gre_single_line.py
@@ -197,6 +197,14 @@ def t1_inv_rec_gre_single_line_kernel(
 
             seq.add_block(pp.make_delay(tr_delay))
 
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
+    seq.set_definition('ReconMatrix', (n_readout, n_phase_encoding, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', te or min_te)
+    seq.set_definition('TR', tr)
+    seq.set_definition('TI', inversion_times.tolist())
+
     return seq, time_to_first_tr_block, min_te
 
 
@@ -273,7 +281,7 @@ def main(
     rf_bwt = 4  # bandwidth-time product of rf excitation pulse [Hz*s]
     rf_apodization = 0.5  # apodization factor of rf excitation pulse
 
-    seq, time_to_first_tr_block, min_te = t1_inv_rec_gre_single_line_kernel(
+    seq, time_to_first_tr_block, _min_te = t1_inv_rec_gre_single_line_kernel(
         system=system,
         inversion_times=inversion_times,
         te=te,
@@ -312,14 +320,6 @@ def main(
         f'{Path(__file__).stem}_{int(fov_xy * 1000)}fov_{n_readout}nx_{n_phase_encoding}ny_{len(inversion_times)}TIs'
     )
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
-    seq.set_definition('ReconMatrix', (n_readout, n_phase_encoding, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', te or min_te)
-    seq.set_definition('TR', tr)
-    seq.set_definition('TI', inversion_times.tolist())
-
     # save seq-file to disk
     output_path = Path.cwd() / 'output'
     output_path.mkdir(parents=True, exist_ok=True)
diff --git a/src/mrseq/sequences/t1_inv_rec_se_single_line.py b/src/mrseq/sequences/t1_inv_rec_se_single_line.py
index 290aaab..eabef5c 100644
--- a/src/mrseq/sequences/t1_inv_rec_se_single_line.py
+++ b/src/mrseq/sequences/t1_inv_rec_se_single_line.py
@@ -258,6 +258,14 @@ def t1_inv_rec_se_single_line_kernel(
 
             seq.add_block(pp.make_delay(tr_delay))
 
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
+    seq.set_definition('ReconMatrix', (n_readout, n_phase_encoding, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', te or min_te)
+    seq.set_definition('TR', tr)
+    seq.set_definition('TI', inversion_times.tolist())
+
     return seq, time_to_first_tr_block, min_te
 
 
@@ -344,7 +352,7 @@ def main(
     rf180_bwt = 4  # bandwidth-time product of rf refocusing pulse [Hz*s]
     rf180_apodization = 0.5  # apodization factor of rf refocusing pulse
 
-    seq, time_to_first_tr_block, min_te = t1_inv_rec_se_single_line_kernel(
+    seq, time_to_first_tr_block, _min_te = t1_inv_rec_se_single_line_kernel(
         system=system,
         inversion_times=inversion_times,
         te=te,
@@ -389,14 +397,6 @@ def main(
         f'{Path(__file__).stem}_{int(fov_xy * 1000)}fov_{n_readout}nx_{n_phase_encoding}ny_{len(inversion_times)}TIs'
     )
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
-    seq.set_definition('ReconMatrix', (n_readout, n_phase_encoding, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', te or min_te)
-    seq.set_definition('TR', tr)
-    seq.set_definition('TI', inversion_times.tolist())
-
     # save seq-file to disk
     output_path = Path.cwd() / 'output'
     output_path.mkdir(parents=True, exist_ok=True)
diff --git a/src/mrseq/sequences/t1_molli_bssfp.py b/src/mrseq/sequences/t1_molli_bssfp.py
index 471bfbe..45979a1 100644
--- a/src/mrseq/sequences/t1_molli_bssfp.py
+++ b/src/mrseq/sequences/t1_molli_bssfp.py
@@ -309,6 +309,15 @@ def t1_molli_bssfp_kernel(
                 # add variable part of trigger delay (soft delay)
                 seq.add_block(trig_soft_delay)
 
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
+    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', te or min_te)
+    seq.set_definition('TR', tr or min_tr)
+    seq.set_definition('TI', inversion_times.tolist())
+    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
+
     return seq, min_te, min_tr
 
 
@@ -401,7 +410,7 @@ def main(
     output_path = Path.cwd() / 'output'
     output_path.mkdir(parents=True, exist_ok=True)
 
-    seq, min_te, min_tr = t1_molli_bssfp_kernel(
+    seq, _min_te, _min_tr = t1_molli_bssfp_kernel(
         system=system,
         te=te,
         tr=tr,
@@ -437,15 +446,6 @@ def main(
         print('\nCreating advanced test report...')
         print(seq.test_report())
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
-    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', te or min_te)
-    seq.set_definition('TR', tr or min_tr)
-    seq.set_definition('TI', inversion_times.tolist())
-    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
-
     # save seq-file to disk
     print(f"\nSaving sequence file '{filename}.seq' into folder '{output_path}'.")
     write_sequence(seq, str(output_path / filename), create_signature=True, v141_compatibility=v141_compatibility)
diff --git a/src/mrseq/sequences/t1_t2_spiral_cmrf.py b/src/mrseq/sequences/t1_t2_spiral_cmrf.py
index 91cf143..8cc8a21 100644
--- a/src/mrseq/sequences/t1_t2_spiral_cmrf.py
+++ b/src/mrseq/sequences/t1_t2_spiral_cmrf.py
@@ -329,6 +329,18 @@ def t1_t2_spiral_cmrf_kernel(
     if mrd_header_file:
         prot.close()
 
+    # write all important parameters into the seq-file definitions
+    seq.set_definition('Name', 'cMRF_spiral')
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
+    seq.set_definition('TE', min_te)
+    seq.set_definition('TI', time_since_inversion)
+    seq.set_definition('TR', tr)
+    seq.set_definition('t2prep_te', [0, 0, t2_prep_echo_times[0], t2_prep_echo_times[1], t2_prep_echo_times[2]])
+    seq.set_definition('t1prep_ti', [time_since_inversion, 0, 0, 0, 0])
+    seq.set_definition('slice_thickness', slice_thickness)
+    seq.set_definition('sampling_scheme', 'spiral')
+    seq.set_definition('number_of_readouts', int(n_readout))
+
     return seq, time_since_inversion, min_te
 
 
@@ -408,7 +420,7 @@ def main(
     if (output_path / Path(filename + '_header.h5')).exists():
         (output_path / Path(filename + '_header.h5')).unlink()
 
-    seq, inversion_time, te = t1_t2_spiral_cmrf_kernel(
+    seq, _inversion_time, _te = t1_t2_spiral_cmrf_kernel(
         system=system,
         t2_prep_echo_times=t2_prep_echo_times,
         tr=tr,
@@ -441,18 +453,6 @@ def main(
         print('\nCreating advanced test report...')
         print(seq.test_report())
 
-    # write all important parameters into the seq-file definitions
-    seq.set_definition('Name', 'cMRF_spiral')
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
-    seq.set_definition('TE', te)
-    seq.set_definition('TI', inversion_time)
-    seq.set_definition('TR', tr)
-    seq.set_definition('t2prep_te', [0, 0, t2_prep_echo_times[0], t2_prep_echo_times[1], t2_prep_echo_times[2]])
-    seq.set_definition('t1prep_ti', [inversion_time, 0, 0, 0, 0])
-    seq.set_definition('slice_thickness', slice_thickness)
-    seq.set_definition('sampling_scheme', 'spiral')
-    seq.set_definition('number_of_readouts', int(n_readout))
-
     # save seq-file to disk
     output_path = Path.cwd() / 'output'
     output_path.mkdir(parents=True, exist_ok=True)
diff --git a/src/mrseq/sequences/t1rho_se_single_line.py b/src/mrseq/sequences/t1rho_se_single_line.py
index d396c84..6bf69d4 100644
--- a/src/mrseq/sequences/t1rho_se_single_line.py
+++ b/src/mrseq/sequences/t1rho_se_single_line.py
@@ -252,6 +252,14 @@ def t1rho_se_single_line_kernel(
 
             seq.add_block(pp.make_delay(tr_delay))
 
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
+    seq.set_definition('ReconMatrix', (n_readout, n_phase_encoding, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', te or min_te)
+    seq.set_definition('TR', tr)
+    seq.set_definition('TSL', spin_lock_times.tolist())
+
     return seq, time_to_first_tr_block, min_te
 
 
@@ -336,7 +344,7 @@ def main(
     rf180_bwt = 4  # bandwidth-time product of rf refocusing pulse [Hz*s]
     rf180_apodization = 0.5  # apodization factor of rf refocusing pulse
 
-    seq, time_to_first_tr_block, min_te = t1rho_se_single_line_kernel(
+    seq, time_to_first_tr_block, _min_te = t1rho_se_single_line_kernel(
         system=system,
         spin_lock_times=spin_lock_times,
         te=te,
@@ -381,14 +389,6 @@ def main(
         f'{Path(__file__).stem}_{int(fov_xy * 1000)}fov_{n_readout}nx_{n_phase_encoding}ny_{len(spin_lock_times)}TIs'
     )
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
-    seq.set_definition('ReconMatrix', (n_readout, n_phase_encoding, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', te or min_te)
-    seq.set_definition('TR', tr)
-    seq.set_definition('TSL', spin_lock_times.tolist())
-
     # save seq-file to disk
     output_path = Path.cwd() / 'output'
     output_path.mkdir(parents=True, exist_ok=True)
diff --git a/src/mrseq/sequences/t2_multi_echo_se_single_line.py b/src/mrseq/sequences/t2_multi_echo_se_single_line.py
index 835ed35..b3321fa 100644
--- a/src/mrseq/sequences/t2_multi_echo_se_single_line.py
+++ b/src/mrseq/sequences/t2_multi_echo_se_single_line.py
@@ -206,6 +206,13 @@ def t2_multi_echo_se_single_line_kernel(
 
             seq.add_block(pp.make_delay(tr_delay))
 
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
+    seq.set_definition('ReconMatrix', (n_readout, n_phase_encoding, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', echo_times.tolist())
+    seq.set_definition('TR', tr)
+
     return seq, min_tr_first_echo_block
 
 
@@ -326,13 +333,6 @@ def main(
     # define sequence filename
     filename = f'{Path(__file__).stem}_{int(fov_xy * 1000)}fov_{n_readout}nx_{n_phase_encoding}ny_{len(echo_times)}TEs'
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
-    seq.set_definition('ReconMatrix', (n_readout, n_phase_encoding, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', echo_times.tolist())
-    seq.set_definition('TR', tr)
-
     # save seq-file to disk
     output_path = Path.cwd() / 'output'
     output_path.mkdir(parents=True, exist_ok=True)
diff --git a/src/mrseq/sequences/t2_t2prep_flash.py b/src/mrseq/sequences/t2_t2prep_flash.py
index 78f9f0a..a22789c 100644
--- a/src/mrseq/sequences/t2_t2prep_flash.py
+++ b/src/mrseq/sequences/t2_t2prep_flash.py
@@ -299,6 +299,14 @@ def t2_t2prep_flash_kernel(
                     # add variable part of trigger delay (soft delay)
                     seq.add_block(trig_soft_delay)
 
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
+    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', te or min_te)
+    seq.set_definition('TR', tr or min_tr)
+    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
+
     return seq, min_te, min_tr
 
 
@@ -399,7 +407,7 @@ def main(
     output_path = Path.cwd() / 'output'
     output_path.mkdir(parents=True, exist_ok=True)
 
-    seq, min_te, min_tr = t2_t2prep_flash_kernel(
+    seq, _min_te, _min_tr = t2_t2prep_flash_kernel(
         system=system,
         te=te,
         tr=tr,
@@ -438,14 +446,6 @@ def main(
         print('\nCreating advanced test report...')
         print(seq.test_report())
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
-    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', te or min_te)
-    seq.set_definition('TR', tr or min_tr)
-    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
-
     # save seq-file to disk
     print(f"\nSaving sequence file '{filename}.seq' into folder '{output_path}'.")
     write_sequence(seq, str(output_path / filename), create_signature=True, v141_compatibility=v141_compatibility)
diff --git a/src/mrseq/sequences/t2star_multi_echo_flash.py b/src/mrseq/sequences/t2star_multi_echo_flash.py
index 46494a4..55a0719 100644
--- a/src/mrseq/sequences/t2star_multi_echo_flash.py
+++ b/src/mrseq/sequences/t2star_multi_echo_flash.py
@@ -317,6 +317,15 @@ def t2star_multi_echo_flash_kernel(
         prot.close()
 
     delta_te_array = np.diff(time_to_echoes)
+
+    # write all required parameters in the seq-file header/definitions
+    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
+    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
+    seq.set_definition('SliceThickness', slice_thickness)
+    seq.set_definition('TE', [(te or float(min_te)) + idx * float(delta_te_array[0]) for idx in range(n_echoes)])
+    seq.set_definition('TR', tr or float(min_tr))
+    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
+
     return seq, float(min_te), float(min_tr), float(delta_te_array[0])
 
 
@@ -420,7 +429,7 @@ def main(
     output_path = Path.cwd() / 'output'
     output_path.mkdir(parents=True, exist_ok=True)
 
-    seq, min_te, min_tr, delta_te = t2star_multi_echo_flash_kernel(
+    seq, _min_te, _min_tr, delta_te = t2star_multi_echo_flash_kernel(
         system=system,
         te=te,
         delta_te=delta_te,
@@ -461,14 +470,6 @@ def main(
         print('\nCreating advanced test report...')
         print(seq.test_report())
 
-    # write all required parameters in the seq-file header/definitions
-    seq.set_definition('FOV', [fov_xy, fov_xy, slice_thickness])
-    seq.set_definition('ReconMatrix', (n_readout, n_readout, 1))
-    seq.set_definition('SliceThickness', slice_thickness)
-    seq.set_definition('TE', [(te or min_te) + idx * delta_te for idx in range(n_echoes)])
-    seq.set_definition('TR', tr or min_tr)
-    seq.set_definition('ReadoutOversamplingFactor', readout_oversampling)
-
     # save seq-file to disk
     print(f"\nSaving sequence file '{filename}.seq' into folder '{output_path}'.")
     write_sequence(seq, str(output_path / filename), create_signature=True, v141_compatibility=v141_compatibility)