Add (multi) 2D EPI kernel and scripts

[schuenke]

To do:

• verify mrd trajectory information for multi-2D acquisitions with and without noise and/or navigator acquisitions
• add tests
• add example scripts
• (optional) replace pulseq-based traj calculation with analytical definition (including ramp sampling and oversampling)
• add frequency offset for ADC in EPI readout
• remove AVG labels from navigator acquisitions and validate ICE recon is still working
• add contact and acknowledgement section to README

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
/home/runner/.local/lib/python3.12/site-packages/mrseq
_version.py	7	7	0%	2–9
/home/runner/.local/lib/python3.12/site-packages/mrseq/preparations
t2_prep.py	51	1	98%	195
/home/runner/.local/lib/python3.12/site-packages/mrseq/scripts
epi2d_fid.py	128	9	93%	261, 364, 421–426, 438, 444
epi2d_se.py	150	12	92%	204–206, 325, 428, 485–490, 502, 508
grpe_flash_dixon.py	205	18	91%	121, 124, 189, 206–208, 330, 349, 400, 410, 503, 571–576, 596, 602
radial_flash.py	140	11	92%	101, 104, 259, 345, 403–408, 428, 434
spiral_flash.py	120	10	92%	95, 231, 313, 363–368, 387, 393
t1_inv_rec_gre_single_line.py	93	9	90%	162, 255, 298–303, 330, 336
t1_inv_rec_se_single_line.py	106	9	92%	219, 316, 375–380, 407, 413
t1_molli_bssfp.py	141	13	91%	216, 282–284, 299, 374, 428–433, 454, 460
t1_t2_spiral_cmrf.py	149	12	92%	89, 95, 114, 168, 385, 432–437, 463, 469
t1rho_se_single_line.py	102	8	92%	310, 367–372, 399, 405
t2_multi_echo_se_single_line.py	96	9	91%	162, 261, 314–319, 344, 350
t2_t2prep_flash.py	143	15	90%	103, 226, 243, 277–279, 291, 367, 429–434, 454, 460
t2star_multi_echo_flash.py	145	14	90%	114, 233, 280–282, 294, 390, 452–457, 477, 483
/home/runner/.local/lib/python3.12/site-packages/mrseq/utils
EpiReadout.py	329	90	73%	52, 61, 193, 197, 244, 318, 322–333, 455, 508–592, 737–743, 763–808
ismrmrd.py	93	2	98%	173, 179
sequence_helper.py	59	4	93%	105, 133–134, 162
trajectory.py	148	3	98%	45, 87, 358
TOTAL	2537	256	90%

Tests	Skipped	Failures	Errors	Time
1493	0 💤	0 ❌	0 🔥	3m 19s ⏱️

[schuenke]

This is how the current version of plot_trajectory() looks like:

symmetric:

flyback:

[ckolbPTB]

In dc500da I changed how the amplitude of the readout gradient is modified for the symmetric EPI readout. In the previous version the EPI-object was modified. This meant that for an odd number of phase encoding steps, the readout gradient of the EPI-object was flipped at the end of add_to_seq. The EPI-object could then not be used anymore to obtain e.g. another repetition. Now the EPI-object is not modified.

I removed the rev-label here:

mrseq/src/mrseq/utils/EpiReadout.py

Line 633 in dc500da

seq.add_block(self.gx, self.adc, lin_label)

I think this should be fine but maybe @schuenke could double check

[ckolbPTB]

Suggested change

pp.make_label(label='AVG', type='SET', value=(n + 1) == 3),

[ckolbPTB]

I would remove this, because it leads to 1 readout having avg = 0 and two readouts with avg = 0,1 which then leads to problems for the MRpro sorting routines. They are not really averages anyway because there is T2* decay.

[ckolbPTB]

Suggested change

pp.make_label(label='AVG', type='SET', value=(n + 1) == 3),

same as for epi2d_fid

[ckolbPTB]

The above changes were necessary to get the correct trajectory for the navigators. Probably similary changes are needed for the epi2d_fid.

We could add the part on reading out the navigators to the example notebook. What do you think @schuenke ?