Dipolar Order Mapping Based on Spin-Lock Magnetic Resonance Imaging.
The 13 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
- [1] § Method › Phantom and In Vivo Studies › Data Processing and Analysis ↔ tractseg/data/dataset_specific_utils.py, lines 13–74 · score 0.98 · ATR_left, ATR_right, AF_right, FPT_left, FPT_right, MLF_left
- [2] § Theory ↔ Function/BMP_solution_ihMT.m, the whole file · a weak match · score 0.91 · local dipolar field, longitudinal relaxation rate, equilibrium magnetizations, exchange rates, dipolar relaxation, frequency offset
- [3] § Theory ↔ Function/cal_RATIO_dosl_acquired.m, lines 40–147 · score 0.77 · absorption lineshape, super Lorentzian, frequency offset, transverse, spin lock, field
- [4] § Method › Simulation Studies › Simulation Study 1: Accuracy of Quantification › Accuracy of Quantification ↔ Simulation_study_1/Accuracry_of_T1D_quantification/Simulation_study1_2.m, lines 31–83 · score 0.72 · 200–800 Hz, ground truth, 2–7 kHz, spin lock, TSL, pulses
- [5] § Method › Acquisition Scheme ↔ Function/cal_RATIO_dosl_acquired.m, lines 40–147 · score 0.71 · ihMT, dual frequency, frequency offsets, spin lock, sequence, duration
- [6] § Results › Simulation Studies ↔ Simulation_study_1/Accuracry_of_T1D_quantification/Simulation_study1_2.m, lines 31–83 · score 0.71 · 200–800 Hz, ground truth, frequency offset, 2–7 kHz, spin lock, duration
- [7] § Method › Calculation of ↔ Simulation_stuty_2/Robustness_B1_B0/Simulation_Study2_2_B1_B0.m, lines 35–66 · score 0.70 · spin lock parameters, RF pulses, water pool, tissue parameters, simulated, model
- [8] § Method › Simulation Studies › Simulation Study 2: Robustness of the Proposed Method › Robustness in Presence of B1 and B0 Inhomogeneity ↔ Simulation_stuty_2/Robustness_B1_B0/Simulation_Study2_2_B1_B0.m, lines 35–66 · score 0.64 · 0.7–1.3, tissue parameters, spin lock, inhomogeneities, robustness, B0
- [9] § Method › Simulation Studies › Simulation Study 1: Accuracy of Quantification › Accuracy of Approximated ↔ Simulation_study_1/Accuracy_of_RATIOdosl/Simulation_study1_1a.m, lines 1–28 · score 0.60 · exact numerical solution, tissue parameters, accuracy, validate, sensitivity, analytical
- [10] § Method › Simulation Studies › Simulation Study 1: Accuracy of Quantification › Accuracy of Approximated ↔ Simulation_study_1/Accuracy_of_RATIOdosl/Simulation_study1_1b.m, lines 1–41 · score 0.60 · exact numerical solution, tissue parameters, accuracy, sensitivity, analytical
- [11] § Results › Simulation Studies ↔ Simulation_study_1/Accuracry_of_T1D_quantification/Simulation_study1_2_plot.m, lines 105–157 · score 0.54 · RF amplitude, ground truth, relative error, quantification, Simulation
- [12] § Theory ↔ Function/BMP_solution_ihMT.m, the whole file · a weak match · score 0.54 · ihMT, relaxation rate, exchange, field, dipolar
- [13] § Method › Simulation Studies › Simulation Study 2: Robustness of the Proposed Method › Robustness Against Noise ↔ Simulation_stuty_2/Robustness_noise/Simulation_stuty2_SNR.m, lines 1–32 · score 0.52 · noise ratio, SNR, signal, Simulated, Robustness
Paper
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The authors' code
MATLAB · 51 lines · 2.1 KB · MIT · 2 matches
- function M_t = BMP_solution_ihMT(t, M, R1a, R2a, dw, w1, w2, kab, kba, M0a, M0b, T2b, R1b, T1d, rfmt)
- % BMP_SOLUTION_IHMT Solves the Bloch-McConnell-Provotorov equations for ihMT.
- %
- % dM/dt = A * M + C
- %
- % Inputs:
- % t - Evolution time duration (s)
- % M - Initial magnetization state vector [Mxa; Mya; Mza; Mzb; Md]
- % R1a - Longitudinal relaxation rate of free pool (1/s)
- % R2a - Transverse relaxation rate of free pool (1/s)
- % dw - Frequency offset (rad/s)
- % w1 - RF amplitude x-component (rad/s)
- % w2 - RF amplitude y-component (rad/s)
- % kab - Exchange rate from pool A to B (1/s)
- % kba - Exchange rate from pool B to A (1/s)
- % M0a - Equilibrium magnetization of free pool
- % M0b - Equilibrium magnetization of bound pool
- % T2b - T2 of bound pool, the lineshape prameter
- % R1b - Longitudinal relaxation rate of bound pool (1/s)
- % T1d - Dipolar relaxation time (s)
- % rfmt - RF saturation rate for the bound pool (1/s)
- %
- % Output:
- % M_t - Magnetization vector at time t
- %% 1. Define Physical Constants
- % Local dipolar field strength (D)
- D = 1/sqrt(15)/T2b;
- % Initial state
- M_init = M;
- %% 2. System Matrix A
- % Represents relaxation, precession, exchange, and RF saturation interactions.
- % State vector: [Mxa, Mya, Mza, Mzb, beta]'
- A = [-R2a, dw, -w2, 0, 0; % Mxa
- -dw, -R2a, w1, 0, 0; % Mya
- w2, -w1, -(R1a + kab), kba, 0; % Mza
- 0, 0, kab, -(R1b + kba + rfmt), rfmt * dw; % Mzb
- 0, 0, 0, rfmt * dw / (D^2), -(1/T1d + rfmt * (dw / D)^2)]; % beta
- %% 3. Recovery Vector C
- % Drives the system towards thermal equilibrium.
- C = [0; 0; R1a * M0a; R1b * M0b; 0];
- %% 4. Analytical Solution
- % Solves the linear differential equation dM/dt = A*M + C
- % Solution: M(t) = exp(A*t) * (M_init - M_ss) + M_ss, where M_ss = -inv(A)*C
- M_t = expm(A * t) * (M_init + A \ C) - A \ C;
- end
BMP_solution_ihMT.m at commit 37033dc, under MIT · at the source
Overview
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Hong Kong
- MR Research Collaboration, Siemens Healthineers Ltd. Hong Kong
Abstract
Inhomogeneous magnetization transfer (ihMT) is sensitive to dipolar order associated with motion‐restricted macromolecules and can be characterized by the dipolar relaxation time T1D. In this study, we propose a spin‐lock MRI framework for T1D quantification. Specifically, we introduce a T1D‐sensitive metric, RATIOdosl, derived from the distinct relaxation rate Rdosl, defined as the difference between dual‐frequency and single‐frequency R1ρ measurements. To enable dual‐frequency spin‐lock acquisition, we developed a dedicated rotary‐echo spin‐lock sequence. Based on this framework, we further estimated T1D and the macromolecular proton fraction (MPF) within a unified acquisition. The proposed method was evaluated using numerical simulations, phantom experiments, and in vivo imaging in the healthy human brain. Simulations demonstrated high sensitivity of RATIOdosl to T1D and supported the robustness of the proposed approach under the investigated conditions. Phantom experiments showed measurable ihMT contrast and supported the feasibility of T1D estimation using RATIOdosl. In vivo experiments demonstrated simultaneous T1D and MPF mapping using only three spin‐lock‐prepared images. Across 10 healthy volunteers, mean white matter T1D values ranged from approximately 3.70 to 4.80 ms. By requiring only three contrast‐prepared images, the proposed technique provides a rapid framework for simultaneous T1D and MPF mapping and may facilitate further investigation of dipolar‐order‐sensitive microstructural imaging in vivo.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above, with 13 matches between paragraphs and lines of code.
zjgao-spin/Dipolar-order-mapping
37033dc67cf77fd9c83797cdc1386149fdd08c7f, 27 June 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
17 files
- Function/
BMP_solution_ihMT.m — MATLAB, 51 lines, 2 matches - Function/
RF_MT.m — MATLAB, 32 lines - Function/
cal_RATIO_dosl_acquired. — MATLAB, 176 lines, 2 matchesm - Function/
cal_RATIO_dosl_approx.m — MATLAB, 16 lines - Function/
cal_RATIO_dosl_exact.m — MATLAB, 51 lines - Function/
cal_T1d_analytical.m — MATLAB, 112 lines - Function/
cal_T1d_dictionary.m — MATLAB, 17 lines - Simulation_study_1/
Accuracry_of_T1D_quantif — MATLAB, 148 lines, 2 matchesication/ Simulation_study1_2.m - Simulation_study_1/
Accuracry_of_T1D_quantif — MATLAB, 232 lines, 1 matchication/ Simulation_study1_2_plot .m - Simulation_study_1/
Accuracy_of_RATIOdosl/ — MATLAB, 257 lines, 1 matchSimulation_study1_1a.m - Simulation_study_1/
Accuracy_of_RATIOdosl/ — MATLAB, 277 lines, 1 matchSimulation_study1_1b.m - Simulation_stuty_2/
Robustness_B1_B0/ — MATLAB, 121 linesSimulation_Study2_1_B1_B 0.m - Simulation_stuty_2/
Robustness_B1_B0/ — MATLAB, 212 lines, 2 matchesSimulation_Study2_2_B1_B 0.m - Simulation_stuty_2/
Robustness_noise/ — MATLAB, 198 lines, 1 matchSimulation_stuty2_SNR.m - Simulation_stuty_2/
Robustness_tissue_parame — MATLAB, 201 linesters/ Simulation_study_2_tissu e.m - LICENSE — License, 21 lines
- README.md — Text, 11 lines
MIC-DKFZ/TractSeg
bff94975b0950385b4880050b8c9a095c7257adb, 23 February 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
108 files
- examples/
.ipynb_checkpoints/ — Jupyter, 68 linesplot_tractometry_results -checkpoint.ipynb - resources/
utility_scripts/ — Python, 1 line__init__.py - resources/
utility_scripts/ — Python, 15 linesapply_brain_mask.py - resources/
utility_scripts/ — Shell, 173 linesdwi_preprocessing.sh - resources/
utility_scripts/ — Python, 38 linesprocess_subjects.py - resources/
utility_scripts/ — Python, 102 linestrk_2_binary.py - setup.py — Python, 45 lines
- tests.sh — Shell, 61 lines
- tests/
__init__.py — Python, 1 line - tests/
reference_files/ — Python, 74 linescreate_toy_streamlines.p y - tests/
reference_files/ — Python, 85 linescreate_toy_streamlines_o ffset_and_invert.py - tests/
test_end_to_end.py — Python, 203 lines - tests/
test_functions.py — Python, 21 lines - tractseg/
__init__.py — Python, 1 line - tractseg/
data/ — Python, 157 linesDLDABG_standalone.py - tractseg/
data/ — Python, 1 line__init__.py - tractseg/
data/ — Python, 52 linescheck_data.py - tractseg/
data/ — Python, 120 linescustom_transformations.p y - tractseg/
data/ — Python, 184 linesdata_loader_inference.py - tractseg/
data/ — Python, 87 linesdata_loader_precomputed. py - tractseg/
data/ — Python, 433 linesdata_loader_training.py - tractseg/
data/ — Python, 159 linesdata_loader_training_3D. py - tractseg/
data/ — Python, 615 lines, 1 matchdataset_specific_utils.p y - tractseg/
data/ — Python, 122 linespreprocessing.py - tractseg/
data/ — Python, 224 linesspatial_transform_custom .py - tractseg/
data/ — Python, 318 linesspatial_transform_peaks. py - tractseg/
data/ — Python, 117 linessubjects.py - tractseg/
experiments/ — Python, 1 line__init__.py - tractseg/
experiments/ — Python, 27 linesbackup/ TractSeg_BX.py - tractseg/
experiments/ — Python, 23 linesbackup/ TractSeg_HR_DAug_Fast_TE ST.py - tractseg/
experiments/ — Python, 121 linesbase.py - tractseg/
experiments/ — Python, 1 linebase_legacy/ __init__.py - tractseg/
experiments/ — Python, 18 linesbase_legacy/ dm_reg_legacy.py - tractseg/
experiments/ — Python, 9 linesbase_legacy/ dm_reg_lowres_legacy.py - tractseg/
experiments/ — Python, 16 linesbase_legacy/ endings_seg_legacy.py - tractseg/
experiments/ — Python, 9 linesbase_legacy/ endings_seg_lowres_legac y.py - tractseg/
experiments/ — Python, 20 linesbase_legacy/ peak_reg_legacy.py - tractseg/
experiments/ — Python, 9 linesbase_legacy/ peak_reg_lowres_legacy.p y - tractseg/
experiments/ — Python, 13 linesbase_legacy/ tract_seg_legacy.py - tractseg/
experiments/ — Python, 9 linesbase_legacy/ tract_seg_lowres_legacy. py - tractseg/
experiments/ — Python, 12 linescustom/ my_custom_experiment.py - tractseg/
experiments/ — Python, 10 linesdm_reg.py - tractseg/
experiments/ — Python, 9 linesdm_reg_lowres.py - tractseg/
experiments/ — Python, 13 linesendings_seg.py - tractseg/
experiments/ — Python, 9 linesendings_seg_lowres.py - tractseg/
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experiments/ — Python, 14 linespeak_reg_angle.py - tractseg/
experiments/ — Python, 9 linespeak_reg_lowres.py - tractseg/
experiments/ — Python, 9 linespretrained_models/ DmReg.py - tractseg/
experiments/ — Python, 29 linespretrained_models/ DmReg_All_BXTensAg_aPTX_ platLR20_noMiss.py - tractseg/
experiments/ — Python, 29 linespretrained_models/ DmReg_All_xtract_PeakRot 4.py - tractseg/
experiments/ — Python, 10 linespretrained_models/ EndingsSeg_PeakRot4.py - tractseg/
experiments/ — Python, 8 linespretrained_models/ Peaks_AngL.py - tractseg/
experiments/ — Python, 7 linespretrained_models/ TractSeg72_888.py - tractseg/
experiments/ — Python, 26 linespretrained_models/ TractSeg_All_BXTensAg_aP TX_platLR20.py - tractseg/
experiments/ — Python, 25 linespretrained_models/ TractSeg_All_xtract_Peak Rot4.py - tractseg/
experiments/ — Python, 16 linespretrained_models/ TractSeg_BXTensAg.py - tractseg/
experiments/ — Python, 26 linespretrained_models/ TractSeg_HR_3D_DAug.py - tractseg/
experiments/ — Python, 15 linespretrained_models/ TractSeg_PeakRot4.py - tractseg/
experiments/ — Python, 8 linespretrained_models/ TractSeg_T1_125mm_DAugAl l.py - tractseg/
experiments/ — Python, 11 linespretrained_models/ TractSeg_T1_12g90g270g_1 25mm_DAugAll.py - tractseg/
experiments/ — Python, 1 linepretrained_models/ __init__.py - tractseg/
experiments/ — Python, 9 linespretrained_models/ old_1/ EndingsSeg_12g90g270g_12 5mm_DAugAll.py - tractseg/
experiments/ — Python, 12 linespretrained_models/ old_1/ Peaks20_12g90g270g_125mm .py - tractseg/
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experiments/ — Python, 9 linespretrained_models/ old_1/ Peaks20_270g_125mm.py - tractseg/
experiments/ — Python, 12 linespretrained_models/ old_1/ Peaks_12g90g270g_125mm_D S_DAugAll.py - tractseg/
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experiments/ — Python, 1 linepretrained_models/ old_1/ __init__.py - tractseg/
experiments/ — Python, 10 linespretrained_models/ old_2/ DmReg_12g90g270g_125mm_D AugAll.py - tractseg/
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experiments/ — Python, 8 linespretrained_models/ old_2/ TractSeg_12g90g270g_125m m_DS_DAugAll_Dropout.py - tractseg/
experiments/ — Python, 1 linepretrained_models/ old_2/ __init__.py - tractseg/
experiments/ — Shell, 39 linesrun_multiple.sh - tractseg/
experiments/ — Python, 10 linestract_seg.py - tractseg/
experiments/ — Python, 9 linestract_seg_lowres.py - tractseg/
libs/ — Python, 186 linesAFQ_MultiCompCorrection. py - tractseg/
libs/ — Python, 1 line__init__.py - tractseg/
libs/ — Python, 147 linescreate_endpoints_mask_wi th_clustering.py - tractseg/
libs/ — Python, 231 linesdata_utils.py - tractseg/
libs/ — Python, 112 linesdirection_merger.py - tractseg/
libs/ — Python, 182 linesexp_utils.py - tractseg/
libs/ — Python, 486 linesfiber_utils.py - tractseg/
libs/ — Python, 708 linesimg_utils.py - tractseg/
libs/ — Python, 382 linesmetric_utils.py - tractseg/
libs/ — Python, 277 linespeak_utils.py - tractseg/
libs/ — Python, 495 linesplot_utils.py - tractseg/
libs/ — Python, 212 linespreprocessing.py - tractseg/
libs/ — Python, 393 linespytorch_einsum.py - tractseg/
libs/ — Python, 327 linespytorch_utils.py - tractseg/
libs/ — Python, 104 linessystem_config.py - tractseg/
libs/ — Python, 259 linestracking.py - tractseg/
libs/ — Python, 201 linestractometry.py - tractseg/
libs/ — Python, 311 linestractseg_prob_tracking.p y - tractseg/
libs/ — Python, 378 linestrainer.py - tractseg/
libs/ — Python, 180 linesutils.py - tractseg/
libs/ — Python, 155 linesvtk_utils.py - tractseg/
models/ — Python, 1 line__init__.py - tractseg/
models/ — Python, 285 linesbase_model.py - tractseg/
models/ — Python, 110 linesunet3d_pytorch_deepsup_s m.py - tractseg/
models/ — Python, 111 linesunet_pytorch.py - tractseg/
models/ — Python, 127 linesunet_pytorch_deepsup.py - tractseg/
models/ — Python, 127 linesunet_pytorch_deepsup_tes t.py - tractseg/
python_api.py — Python, 253 lines - tractseg/
resources/ — Python, 1 line__init__.py - LICENSE — License, 201 lines
- Readme.md — Text, 419 lines
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Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 3 keywords, 6 MeSH terms, 1 funder, 45 references.
Cite
This paper
Gao, Z., Shan, Q., Zhou, Z., Yu, Z., & Chen, W. (2026). Dipolar Order Mapping Based on Spin-Lock Magnetic Resonance Imaging. NMR in biomedicine, 39(7), e70331. https://
BibTeX
@article{gao2026dipolar,
author = {Gao, Zijian and Shan, Qianxue and Zhou, Ziqin and Yu, Ziqiang and Chen, Weitian},
title = {{Dipolar Order Mapping Based on Spin-Lock Magnetic Resonance Imaging}},
journal = {NMR in biomedicine},
year = {2026},
month = jul,
volume = {39},
number = {7},
pages = {e70331},
publisher = {Wiley},
issn = {0952-3480},
doi = {10.1002/
url = {https://
pmid = {42309541},
pmcid = {PMC13275185}
}
RIS
TY - JOUR
AU - Gao, Zijian
AU - Shan, Qianxue
AU - Zhou, Ziqin
AU - Yu, Ziqiang
AU - Chen, Weitian
TI - Dipolar Order Mapping Based on Spin-Lock Magnetic Resonance Imaging
T2 - NMR in biomedicine
J2 - NMR Biomed
PY - 2026
DA - 2026/
VL - 39
IS - 7
SP - e70331
SN - 0952-3480
PB - Wiley
DO - 10.1002/
UR - https://
LA - en
ER -
CSL-JSON
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"container-title": "NMR in biomedicine",
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{
"family": "Gao",
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{
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"given": "Ziqin"
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{
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"family": "Chen",
"given": "Weitian"
}
],
"container-title-short":
"volume": "39",
"issue": "7",
"page": "e70331",
"DOI": "10.1002/
"PMID": "42309541",
"PMCID": "PMC13275185",
"ISSN": "0952-3480",
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"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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2026,
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1
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]
}
}
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