Current State-of-the-Art 3D MRI Sequences for Assessing Bone Morphology with Emphasis on Cranial and Spinal Imaging: A Narrative Review

Abstract

Background

Traditionally, CT has been the go-to method for visualizing bone structures, while MRI has been preferred for assessing soft tissues, because structures containing tightly bound water molecules – such as bones, tendons, cartilage, and ligaments – produce a rapidly decaying T2* signal, which conventional MRI sequences fail to capture. To address this limitation, spoiled gradient echo sequences were refined, and short-TE sequences were introduced, enabling radiation-free bone imaging. This advance is particularly crucial for pediatric patients and in scenarios where an MRI-only approach is preferred, such as in radiation-sensitive cases and surgical planning.

Methods

A comprehensive literature review was conducted by searching the PubMed and Google Scholar databases, using specific keywords: “black bone MRI” or “sCT bone” (Synthetic CT), “ZTE” (zero echo time), “UTE” (ultrashort echo time), “VIBE” (Volumetric Interpolated Breath-hold Examination), “FRACTURE” (FFE resembling a CT using restricted echo-spacing) and for title and abstract queries. The selection criteria included scientific articles published in English and German. The research was focused on the advances of the past five years in the application of the sequences in the area of the skull and spine. To support the technical understanding, earlier publications were also examined to offer readers essential background on the fundamental principles of the sequences, helping them better comprehend recent advances. For the investigation of the recent applications of the sequences, a narrow five-year time frame was applied, resulting in approximately 250 findings. From these, publications focused on the skull and spine regions were selected, with an emphasis on covering various pathologies and a preference for studies that compare different gradient echo sequences. To explore the technical aspects of the sequences, a broader time frame of ten years was selected, yielding approximately 868 results. From these, studies with more general explanations – avoiding in-depth physical and computer science details – were chosen. Using these selection parameters, 69 studies were highlighted.

Results/conclusion

The gradient echo technique enables rapid and adaptable imaging, which can be customized to highlight specific tissue types. Spoiled GRE sequences such as VIBE, STAR/VIBE, and FRACTURE provide enhanced bone-to-soft tissue contrast, particularly when used with Dixon reconstruction. Short-TE sequences like UTE and ZTE utilize fast gradient switching, low flip angles, and non-Cartesian acquisition to improve bone visualization while suppressing soft tissue signals. These methods can effectively detect traumatic, neoplastic, and degenerative changes, offering CT-like imaging capabilities when patient-specific factors and the region or pathology of interest are properly considered. Additionally, integrating bone-selective sequences with deep learning could further enhance diagnostic accuracy and potentially replace CT.

Key Points

• Short TE-sequences achieve better bone/soft tissue contrast, but are more computationally demanding.

• ZTE is the sequence of choice for skull vault pathology, preoperative spine and skull imaging and is a preferable base for neural networks in sCT generation.

• Modified UTE sequences excel in viscerocranium and spine imaging DURANDE for bone/air-interface, 3D-stack of stars UTE with Dixon reconstruction for spine pathologies, replacing the conventional MRI sequences.

• VIBE/STAR-VIBE for facial preoperative and traumatic imaging, where motion artifacts are problematic.

• Bone and ligament matrix quantification with Dual echo and IR-UTE-Cones sequence, emitting porosity index, suppression ratio, and mapping values.

Citation Format

• Kavrakova IG, Haage P, Stueckle CA. Current State-of-the-Art 3D MRI Sequences for Assessing Bone Morphology with Emphasis on Cranial and Spinal Imaging: A Narrative Review. Rofo 2025; DOI 10.1055/a-2673-4339

Zusammenfassung

Hintergrund

Traditionell galt die CT als bevorzugte Methode zur Darstellung von Knochenstrukturen, während die MRT vor allem zur Beurteilung von Weichteilen eingesetzt wurde. Dies liegt daran, dass Gewebe mit stark gebundenen Wassermolekülen – wie Knochen, Sehnen, Knorpel und Bänder – ein schnell zerfallendes T2*-Signal erzeugen, das von konventionellen MRT-Sequenzen nicht erfasst wird. Um diese Einschränkung zu überwinden, wurden Spoiled-Gradienten-Echo-Sequenzen weiterentwickelt und Sequenzen mit sehr kurzer Echozeit eingeführt, die eine strahlungsfreie Knochendarstellung ermöglichen.

Methoden

Eine gezielte Literaturrecherche in den Datenbanken PubMed und Google Scholar wurde mit den Schlagwörtern „blackbone MRI“, „sCT bone“, „ZTE“, „UTE“, „VIBE“ und „FRACTURE“ durchgeführt. Berücksichtigt wurden englisch- und deutschsprachige Artikel, mit Schwerpunkt auf Studien der letzten fünf Jahre zur Anwendung dieser Sequenzen an Schädel und Wirbelsäule. Zur technischen Einordnung wurden ergänzend ältere Arbeiten herangezogen. Insgesamt ergab die Suche rund 250 relevante Studien zur klinischen Anwendung und 868 zur technischen Grundlage. Nach Auswahlkriterien wurden 69 Studien einbezogen.

Ergebnisse und Schlussfolgerung

Gradientenecho-Techniken wie VIBE, STAR-VIBE und FRACTURE (mit Dixon) verbessern den Knochen-Weichteil-Kontrast. Short-TE-Sequenzen wie ZTE und UTE unterdrücken Weichteilsignale und erlauben eine präzise Knochendarstellung. In Kombination mit KI-Methoden bieten sie langfristig eine strahlungsfreie Alternative zur CT bei traumatischen, neoplastischen und degenerativen Veränderungen.

Kernaussagen

• ZTE ist die bevorzugte Sequenz bei Pathologien des Schädeldachs, präoperativer Bildgebung und für die Erstellung von synthetischem CT (sCT).

• Modifizierte UTE-Sequenzen eignen sich besonders gut für die Bildgebung des Viszerokraniums (DURANDE) und der Wirbelsäule (3D-Stack of Stars UTE mit Dixon-Rekonstruktion).

• VIBE/STAR-VIBE werden für die präoperative und traumatische Gesichtsbildgebung verwendet.

• Quantifizierung der Knochen- und Bandmatrix mit Dual-Echo und IR-Cones-UTE, wobei Parameter wie Porositätsindex, Suppressionsverhältnis und Mapping-Werte ermittelt werden.

Keywords

BlackBone MRI - ZTE - UTE - VIBE - FRACTURE - sCT

Publikationsverlauf

Eingereicht: 08. April 2025

Angenommen nach Revision: 19. Juli 2025

Artikel online veröffentlicht:
17. September 2025

• References

• 1 Soldati E, Rossi F, Vicente J. et al. Survey of MRI Usefulness for the Clinical Assessment of Bone Microstructure. Int J Mol Sci 2021; 22
• 2 Techawiboonwong A, Song HK, Magland JF. et al. Implications of pulse sequence in structural imaging of trabecular bone. J Magn Reson Imaging 2005; 22: 647-655
• 3 Larson PE, Han M, Krug R. et al. Ultrashort echo time and zero echo time MRI at 7T. MAGMA 2016; 29: 359-370
• 4 Wiesinger F, Ho ML. Zero-TE MRI: Principles and applications in the head and neck. Br J Radiol 2022; 95: 20220059
• 5 Holmes JE, Bydder GM. MR imaging with ultrashort TE (UTE) pulse sequences: Basic principles. Radiography 2005; 11: 163-74
• 6 More Sa XZ. Ultrashort echo time and zero echo time MR imaging and their applications at high magnetic fields: A literature survey. 2019, Molecular Imaging and Biology 6: 1003-1019 2022;
• 7 Ljungberg E, Damestani NL, Wood TC. et al. Silent zero TE MR neuroimaging: Current state-of-the-art and future directions. Prog Nucl Magn Reson Spectrosc 2021; 123: 73-93
• 8 Katakura M, Mitchell AWM, Lee JC. et al. Is it time to replace CT with T1-VIBE MRI for the assessment of musculoskeletal injuries?. Bone Joint J 2020; 102-B: 1435-1437
• 9 Ma J. Dixon techniques for water and fat imaging. J Magn Reson Imaging 2008; 28: 543-558
• 10 Dremmen MHG, Wagner MW, Bosemani T. et al. Does the Addition of a “Black Bone” Sequence to a Fast Multisequence Trauma MR Protocol Allow MRI to Replace CT after Traumatic Brain Injury in Children?. AJNR Am J Neuroradiol 2017; 38: 2187-2192
• 11 Kamona N, Jones BC, Lee H. et al. Cranial bone imaging using ultrashort echo-time bone-selective MRI as an alternative to gradient-echo based “black-bone” techniques. MAGMA 2024; 37: 83-92
• 12 Patel KB, Eldeniz C, Skolnick GB. et al. 3D pediatric cranial bone imaging using high-resolution MRI for visualizing cranial sutures: A pilot study. J Neurosurg Pediatr 2020; 26: 311-317
• 13 Gascho D, Zoelch N, Tappero C. et al. FRACTURE MRI: Optimized 3D multi-echo in-phase sequence for bone damage assessment in craniocerebral gunshot injuries. Diagn Interv Imaging 2020; 101: 611-615
• 14 Feuerriegel GC, Kronthaler S, Boehm C. et al. Diagnostic value of water-fat-separated images and CT-like susceptibility-weighted images extracted from a single ultrashort echo time sequence for the evaluation of vertebral fractures and degenerative changes of the spine. Eur Radiol 2023; 33: 1445-1455
• 15 Ang EC, Robertson AF, Malara FA. et al. Diagnostic accuracy of 3-T magnetic resonance imaging with 3D T1 VIBE versus computer tomography in pars stress fracture of the lumbar spine. Skeletal Radiol 2016; 45: 1533-1540
• 16 Lecouvet FE, Zan D, Lepot D. et al. MRI-based Zero Echo Time and Black Bone Pseudo-CT Compared with Whole-Body CT to Detect Osteolytic Lesions in Multiple Myeloma. Radiology 2024; 313: e231817
• 17 Deininger-Czermak E, Gascho D, Franckenberg S. et al. Added value of ultra-short echo time and fast field echo using restricted echo-spacing MR imaging in the assessment of the osseous cervical spine. Radiol Med 2023; 128: 234-241
• 18 Florkow MC, Zijlstra F, Willemsen K. et al. Deep learning-based MR-to-CT synthesis: The influence of varying gradient echo-based MR images as input channels. Magn Reson Med 2020; 83: 1429-1441
• 19 Getzmann JM, Deininger-Czermak E, Melissanidis S. et al. Deep learning-based pseudo-CT synthesis from zero echo time MR sequences of the pelvis. Insights Imaging 2024; 15: 202
• 20 Jerban S, Ma Y, Alenezi S. et al. Ultrashort Echo Time (UTE) MRI porosity index (PI) and suppression ratio (SR) correlate with the cortical bone microstructural and mechanical properties: Ex vivo study. Bone 2023; 169: 116676
• 21 Jerban S, Ma Y, Moazamian D. et al. MRI-based porosity index (PI) and suppression ratio (SR) in the tibial cortex show significant differences between normal, osteopenic, and osteoporotic female subjects. Front Endocrinol (Lausanne) 2023; 14: 1148345
• 22 Liu J, Liao JW, Li W. et al. Assessment of Osteoporosis in Lumbar Spine: In Vivo Quantitative MR Imaging of Collagen Bound Water in Trabecular Bone. Front Endocrinol (Lausanne) 2022; 13: 801930
• 23 Marco Ravanelli DF, Roberto Maroldi. FREEZEit StarVIBE: Freezing the MovingHead and Neck at a Sub-millimetric Scal. MAGNETOM Flash | (66) 3/2016 |. http://www.siemens.com/magnetom-world 2016
• 24 Johnson B, Alizai H, Dempsey M. Fast field echo resembling a CT using restricted echo-spacing (FRACTURE): A novel MRI technique with superior bone contrast. Skeletal Radiol 2021; 50: 1705-1713
• 25 der Meulen P, Groen JP, Tinus AM. et al. Fast Field Echo imaging: An overview and contrast calculations. Magn Reson Imaging 1988; 6: 355-368
• 26 Wang N, Jin Z, Liu F. et al. Bone injury imaging in knee and ankle joints using fast-field-echo resembling a CT using restricted echo-spacing MRI: A feasibility study. Front Endocrinol (Lausanne) 2024; 15: 1421876
• 27 Athertya JS, Ma Y, Masoud Afsahi A. et al. Accelerated Quantitative 3D UTE-Cones Imaging Using Compressed Sensing. Sensors (Basel) 2022; 22
• 28 Shen X, Ozen AC, Sunjar A. et al. Ultra-short T(2) components imaging of the whole brain using 3D dual-echo UTE MRI with rosette k-space pattern. Magn Reson Med 2023; 89: 508-521
• 29 McRobbie DW, Moore EA, Graves MJ. The Parallel Universe: Parallel Imaging and Novel Acquisition Techniques. In: MRI from picture to proton. In: . Cambridge: Cambridge University Press; 2017: 225-250
• 30 McRobbie DW, Moore EA, Graves MJ. Let’s Talk Technical: MR Equipment. In: MRI from picture to proton. In: . Cambridge: Cambridge University Press; 2017: 144-165
• 31 Bambach S, Ho ML. Deep Learning for Synthetic CT from Bone MRI in the Head and Neck. AJNR Am J Neuroradiol 2022; 43: 1172-1179
• 32 Froidevaux R, Weiger M, Brunner DO. et al. Filling the dead-time gap in zero echo time MRI: Principles compared. Magn Reson Med 2018; 79: 2036-2045
• 33 Eley KA, McIntyre AG, Watt-Smith SR. et al. “Black bone” MRI: A partial flip angle technique for radiation reduction in craniofacial imaging. Br J Radiol 2012; 85: 272-278
• 34 Shin SH, Chae HD, Suprana A. et al. UTE MRI technical developments and applications in osteoporosis: a review. Front Endocrinol (Lausanne) 2025; 16: 1510010
• 35 Jones BC, Jia S, Lee H. et al. MRI-derived porosity index is associated with whole-bone stiffness and mineral density in human cadaveric femora. Bone 2021; 143: 115774
• 36 Du J, Bydder GM. Qualitative and quantitative ultrashort-TE MRI of cortical bone. NMR Biomed 2013; 26: 489-506
• 37 Hamwood J, Schmutz B, Collins MJ. et al. A deep learning method for automatic segmentation of the bony orbit in MRI and CT images. Sci Rep 2021; 11: 13693
• 38 Pak Lun Kevin Ding ZL, Yuxiang Zhou. et al. Deep residual dense U-Net for resolution enhancement in accelerated MRI acquisition. Medical Imaging 2019: Image Processing. SPIE Medical Imaging, 2019, San Diego, California, US; 2019;
• 39 Jans LBO, Chen M, Elewaut D. et al. MRI-based Synthetic CT in the Detection of Structural Lesions in Patients with Suspected Sacroiliitis: Comparison with MRI. Radiology 2021; 298: 343-349
• 40 Upadhyay J, Iwasaka-Neder J, Golden E. et al. Synthetic CT Assessment of Lesions in Children With Rare Musculoskeletal Diseases. Pediatrics 2023; 152
• 41 Achar S, Hwang D, Finkenstaedt T. et al. Deep-Learning-Aided Evaluation of Spondylolysis Imaged with Ultrashort Echo Time Magnetic Resonance Imaging. Sensors (Basel) 2023; 23
• 42 Tan AP. MRI Protocol for Craniosynostosis: Replacing Ionizing Radiation-Based CT. AJR Am J Roentgenol 2019; 213: 1374-1380
• 43 Low XZ, Lim MC, Nga V. et al. Clinical application of “black bone” imaging in paediatric craniofacial disorders. Br J Radiol 2021; 94: 20200061
• 44 Deininger-Czermak E, Euler A, Franckenberg S. et al. Evaluation of ultrashort echo-time (UTE) and fast-field-echo (FRACTURE) sequences for skull bone visualization and fracture detection: A postmortem study. J Neuroradiol 2022; 49: 237-243
• 45 Lu A, Gorny KR, Ho ML. Zero TE MRI for Craniofacial Bone Imaging. AJNR Am J Neuroradiol 2019; 40: 1562-1566
• 46 Aydingoz U, Yildiz AE, Ergen FB. Zero Echo Time Musculoskeletal MRI: Technique, Optimization, Applications, and Pitfalls. Radiographics 2022; 42: 1398-1414
• 47 Koh E, Walton ER, Watson P. VIBE MRI: An alternative to CT in the imaging of sports-related osseous pathology?. Br J Radiol 2018; 91: 20170815
• 48 Tsuchiya K, Gomyo M, Katase S. et al. Magnetic resonance bone imaging: Applications to vertebral lesions. Jpn J Radiol 2023; 41: 1173-1185
• 49 Schiettecatte E, Vereecke E, Jaremko JL. et al. MRI-based synthetic CT for assessment of the bony elements of the sacroiliac joints in children. Insights Imaging 2024; 15: 53
• 50 Schwaiger BJ, Schneider C, Kronthaler S. et al. CT-like images based on T1 spoiled gradient-echo and ultra-short echo time MRI sequences for the assessment of vertebral fractures and degenerative bone changes of the spine. Eur Radiol 2021; 31: 4680-4689
• 51 Hoving AM, Kraeima J, Schepers RH. et al. Optimisation of three-dimensional lower jaw resection margin planning using a novel Black Bone magnetic resonance imaging protocol. PLoS One 2018; 13: e0196059
• 52 Burian E, Sollmann N, Ritschl LM. et al. High resolution MRI for quantitative assessment of inferior alveolar nerve impairment in course of mandible fractures: An imaging feasibility study. Sci Rep 2020; 10: 11566
• 53 Altorfer FCS, Burkhard MD, Kelly MJ. et al. Robot-Assisted Lumbar Pedicle Screw Placement Based on 3D Magnetic Resonance Imaging. Global Spine J 2025; 15: 1243-1250
• 54 Wei Z, Lombardi AF, Lee RR. et al. Comprehensive assessment of in vivo lumbar spine intervertebral discs using a 3D adiabatic T(1rho) prepared ultrashort echo time (UTE-Adiab-T(1rho)) pulse sequence. Quant Imaging Med Surg 2022; 12: 269-280
• 55 Florkow MC, Willemsen K, Mascarenhas VV. et al. Magnetic Resonance Imaging Versus Computed Tomography for Three-Dimensional Bone Imaging of Musculoskeletal Pathologies: A Review. J Magn Reson Imaging 2022; 56: 11-34
• 56 Afsahi AM, Lombardi AF, Wei Z. et al. High-Contrast Lumbar Spinal Bone Imaging Using a 3D Slab-Selective UTE Sequence. Front Endocrinol (Lausanne) 2021; 12: 800398
• 57 Wolharn L, Guggenberger R, Higashigaito K. et al. Detailed bone assessment of the sacroiliac joint in a prospective imaging study: Comparison between computed tomography, zero echo time, and black bone magnetic resonance imaging. Skeletal Radiol 2022; 51: 2307-2315
• 58 Burian E, Probst FA, Weidlich D. et al. MRI of the inferior alveolar nerve and lingual nerve-anatomical variation and morphometric benchmark values of nerve diameters in healthy subjects. Clin Oral Investig 2020; 24: 2625-2634
• 59 Staartjes VE, Seevinck PR, Vandertop WP. et al. Magnetic resonance imaging-based synthetic computed tomography of the lumbar spine for surgical planning: A clinical proof-of-concept. Neurosurg Focus 2021; 50: E13
• 60 Inoue A, Watanabe H, Suehiro S. et al. Clinical utility of new bone imaging using zero-echo-time sequence in neurosurgical procedures: Can zero-echo-time be used in clinical practice in neurosurgery?. Neuroradiol J 2023; 36: 289-296
• 61 Link TM, Kazakia G. Update on Imaging-Based Measurement of Bone Mineral Density and Quality. Curr Rheumatol Rep 2020; 22: 13
• 62 Ren C, Zhu Q, Li Q. et al. Assessment of the sacroiliac joint in patients with axial spondyloarthritis via three-dimensional ultrashort echo time magnetic resonance imaging. Quant Imaging Med Surg 2024; 14: 4141-4154
• 63 Wu LL, Liu LH, Rao SX. et al. Ultrashort time-to-echo T2* and T2* relaxometry for evaluation of lumbar disc degeneration: A comparative study. BMC Musculoskelet Disord 2022; 23: 524
• 64 Lombardi AF, Wei Z, Wong J. et al. High contrast cartilaginous endplate imaging using a 3D adiabatic inversion-recovery-prepared fat-saturated ultrashort echo time (3D IR-FS-UTE) sequence. NMR Biomed 2021; 34: e4579
• 65 Chen KC, Siriwananrangsun P, Bae WC. Ultrashort-Echo-Time MRI of the Disco-Vertebral Junction: Modulation of Image Contrast via Echo Subtraction and Echo Times. Sensors (Basel) 2024; 24
• 66 Kassey VB, Walle M, Egan J. et al. Quantitative (31)P magnetic resonance imaging on pathologic rat bones by ZTE at 7T. Bone 2024; 180: 116996
• 67 Kassey VB, Walle M, Egan J. et al. Quantitative (1)H Magnetic Resonance Imaging on Normal and Pathologic Rat Bones by Solid-State (1)H ZTE Sequence with Water and Fat Suppression. J Magn Reson Imaging 2024; 60: 2423-2432
• 68 McRobbie DW, Moore EA, Graves MJ. Acronyms Anonymous II: Gradient Echo. In: MRI from picture to proton. In: . Cambridge: Cambridge University Press; 2017: 207-224
• 69 Chavhan GB, Babyn PS, Jankharia BG. et al. Steady-state MR imaging sequences: Physics, classification, and clinical applications. Radiographics 2008; 28: 1147-1160