Characterizing geometric distortions of 3D sequences in clinical head MRI

Objective Phantoms are often used to estimate the geometric accuracy in magnetic resonance imaging (MRI). However, the distortions may differ between anatomical and phantom images. This study aimed to investigate the applicability of a phantom-based and a test-subject-based method in evaluating geometric distortion present in clinical head-imaging sequences. Materials and methods We imaged a 3D-printed phantom and test subjects with two MRI scanners using two clinical head-imaging 3D sequences with varying patient-table positions and receiver bandwidths. The geometric distortions were evaluated through nonrigid registrations: the displaced acquisitions were compared against the ideal isocenter positioning, and the varied bandwidth volumes against the volume with the highest bandwidth. The phantom acquisitions were also registered to a computed tomography scan. Results Geometric distortion magnitudes increased with larger table displacements and were in good agreement between the phantom and test-subject acquisitions. The effect of increased distortions with decreasing receiver bandwidth was more prominent for test-subject acquisitions. Conclusion Presented results emphasize the sensitivity of the geometric accuracy to positioning and imaging parameters. Phantom limitations may become an issue with some sequence types, encouraging the use of anatomical images for evaluating the geometric accuracy.Peer reviewe

Methods for evaluating geometric distortion in magnetic resonance imaging

Abstract. Geometric distortions and spatial inaccuracies in magnetic resonance imaging are an important concern especially in image-guided high accuracy operations, such as radiotherapy or stereotactic surgeries. Geometric distortions in the images are in principle caused by erroneous spatial encoding of the signal echo. Errors in the spatial encoding are caused by different physical factors, such as static field inhomogeneity, gradient field nonlinearities, chemical shift, and magnetic susceptibility. The distortion shifts can be quantitatively evaluated as the amount of distance or pixels that a signal source has shifted in the mapping from real space to the image space. By studying the distortions and the causing mechanisms, corrective measures can be taken to minimize spatial errors in the images. In this thesis the geometric distortions of one MRI scanner are evaluated with four different grid phantom objects. The scanner was a 3 Tesla scanner at the Oulu University Hospital. The phantoms included two commercial readily available MRI quality assurance phantoms and two in-house produced prototype phantoms. The methods consisted of imaging the phantoms with different two- and three- dimensional sequences. Image and distortion analysis was performed with one commercial distortion check software for the respective commercial phantom, and with an in-house developed Matlab program for all four phantoms. Results for the magnitude and direction of the distortion as a function of distance from the scanner isocenter were acquired. Three-dimensional distortion shifts up 4 mm within a radius of 200 mm from the isocenter were measured, with occasional shifts up to 9 mm between 100 and 200 mm from the isocenter. Distortion field maps and contour plots produced with both analysis methods seemed to be in accordance with each other, and the geometry and behaviour of the field was found to be as expected. As to the prototype phantoms, a result with respect to the grid density was found. A 5 mm grid separation was too dense with respect to the achievable resolution for the Matlab analysis script to function, or more generally for any distortion check at all.Tiivistelmä. Magneettikuvien geometriset vääristymät ja epätarkkuudet ovat tärkeitä huomioon otettavia asioita erityisesti sädehoitoihin tai kirurgisiin operaatioihin liittyvissä kuvantamisissa. Kuvien vääristymät aiheutuvat virheistä signaalien paikkakoodauksessa. Paikkakoodaukseen aiheutuu virheitä eri fysikaalisista tekijöistä, kuten staattisen magneettikentän epähomogeenisuuksista, gradienttikenttien epälineaarisuuksista, kemiallisesta siirtymästä tai magneettisesta suskeptibiliteetistä. Geometrinen vääristymä voidaan määrittää kvantitatiivisesti tutkimalla signaalin paikan siirtymää kuvauksessa todellisesta koordinaatistosta, eli kuvattavasta kohteesta, kuvan koordinaatistoon. Kuvia voidaan myös korjata vääristymien osalta tutkimalla vääristymien luonnetta ja niiden aiheuttajia. Tässä tutkielmassa tutkittiin Oulun yliopistollisen sairaalan yhden 3 Teslan kenttävoimakkuuden magneettikuvauslaitteen geometrista vääristymää. Kuvauksissa käytettiin neljää erilaista fantomia, kahta valmista kaupallisesti saatavilla olevaa sekä kahta kokeellista prototyyppiä. Fantomeita kuvattiin eri kaksi- ja kolmiulotteisilla kuvaussekvensseillä. Kuva- ja vääristymäanalyysiä varten käytettiin yhtä kaupallista ohjelmaa, joka on tarkoitettu sitä vastaavalle fantomille, sekä itse sairaalassa kehitettyä Matlab-pohjaista ohjelmaa. Mittausten perusteella saatiin kvantitatiiviset tulokset vääristymän suuruudelle ja suunnalle, etäisyyden funktiona skannerin keskipisteestä. Kolmiulotteisten vääristymien suuruudet olivat 4 mm tai alle 200 mm säteelle asti, suurimpien yksittäisten vääristymien ollessa noin 9 mm tai alle 100 mm ja 200 mm etäisyyksien välillä. Molemmilla analyysiohjelmilla vääristymien suuntien perusteella luodut vektorikentät olivat toistensa mukaisia ja vääristymän käyttäytyminen vaikutti odotetulta. Prototyyppifantomien suhteen päädyttiin tulokseen, jonka mukaan 5 mm ruudukko oli liian tiheä suhteessa resoluutioon, eikä Matlab-pohjainen analyysi toiminut. Tarpeeksi leveä ruudukko oli siten oleellinen osa vääristymän määrittämistä

Motion modeling from 4D MR images of liver simulating phantom

Background and purpose A novel method of retrospective liver modeling was developed based on four-dimensional magnetic resonance (4D-MR) images. The 4D-MR images will be utilized in generation of the subject-specific deformable liver model to be used in radiotherapy planning (RTP). The purpose of this study was to test and validate the developed 4D-magnetic resonance imaging (MRI) method with extensive phantom tests. We also aimed to build a motion model with image registration methods from liver simulating phantom images. Materials and methods A deformable phantom was constructed by combining deformable tissue-equivalent material and a programmable 4D CIRS-platform. The phantom was imaged in 1.5 T MRI scanner with T2-weighted 4D SSFSE and T1-weighted Ax dual-echo Dixon SPGR sequences, and in computed tomography (CT). In addition, geometric distortion of the 4D sequence was measured with a GRADE phantom. The motion model was developed; the phases of the 4D-MRI were used as surrogate data, and displacement vector fields (DVF's) were used as a motion measurement. The motion model and the developed 4D-MRI method were evaluated and validated with extensive tests. Result The 4D-MRI method enabled an accuracy of 2 mm using our deformable phantom compared to the 4D-CT. Results showed a mean accuracy of <2 mm between coordinates and DVF's measured from the 4D images. Three-dimensional geometric accuracy results with the GRADE phantom were: 0.9-mm mean and 2.5 mm maximum distortion within a 100 mm distance, and 2.2 mm mean, 5.2 mm maximum distortion within a 150 mm distance from the isocenter. Conclusions The 4D-MRI method was validated with phantom tests as a necessary step before patient studies. The subject-specific motion model was generated and will be utilized in the generation of the deformable liver model of patients to be used in RTP.Background and purpose A novel method of retrospective liver modeling was developed based on four-dimensional magnetic resonance (4D-MR) images. The 4D-MR images will be utilized in generation of the subject-specific deformable liver model to be used in radiotherapy planning (RTP). The purpose of this study was to test and validate the developed 4D-magnetic resonance imaging (MRI) method with extensive phantom tests. We also aimed to build a motion model with image registration methods from liver simulating phantom images. Materials and methods A deformable phantom was constructed by combining deformable tissue-equivalent material and a programmable 4D CIRS-platform. The phantom was imaged in 1.5 T MRI scanner with T2-weighted 4D SSFSE and T1-weighted Ax dual-echo Dixon SPGR sequences, and in computed tomography (CT). In addition, geometric distortion of the 4D sequence was measured with a GRADE phantom. The motion model was developed; the phases of the 4D-MRI were used as surrogate data, and displacement vector fields (DVF's) were used as a motion measurement. The motion model and the developed 4D-MRI method were evaluated and validated with extensive tests. Result The 4D-MRI method enabled an accuracy of 2 mm using our deformable phantom compared to the 4D-CT. Results showed a mean accuracy ofPeer reviewe

Cost-effective non-destructive testing of biomedical components fabricated using additive manufacturing

Biocompatible titanium-alloys can be used to fabricate patient-specific medical components using additive manufacturing (AM). These novel components have the potential to improve clinical outcomes in various medical scenarios. However, AM introduces stability and repeatability concerns, which are potential roadblocks for its widespread use in the medical sector. Micro-CT imaging for non-destructive testing (NDT) is an effective solution for post-manufacturing quality control of these components. Unfortunately, current micro-CT NDT scanners require expensive infrastructure and hardware, which translates into prohibitively expensive routine NDT. Furthermore, the limited dynamic-range of these scanners can cause severe image artifacts that may compromise the diagnostic value of the non-destructive test. Finally, the cone-beam geometry of these scanners makes them susceptible to the adverse effects of scattered radiation, which is another source of artifacts in micro-CT imaging. In this work, we describe the design, fabrication, and implementation of a dedicated, cost-effective micro-CT scanner for NDT of AM-fabricated biomedical components. Our scanner reduces the limitations of costly image-based NDT by optimizing the scanner\u27s geometry and the image acquisition hardware (i.e., X-ray source and detector). Additionally, we describe two novel techniques to reduce image artifacts caused by photon-starvation and scatter radiation in cone-beam micro-CT imaging. Our cost-effective scanner was designed to match the image requirements of medium-size titanium-alloy medical components. We optimized the image acquisition hardware by using an 80 kVp low-cost portable X-ray unit and developing a low-cost lens-coupled X-ray detector. Image artifacts caused by photon-starvation were reduced by implementing dual-exposure high-dynamic-range radiography. For scatter mitigation, we describe the design, manufacturing, and testing of a large-area, highly-focused, two-dimensional, anti-scatter grid. Our results demonstrate that cost-effective NDT using low-cost equipment is feasible for medium-sized, titanium-alloy, AM-fabricated medical components. Our proposed high-dynamic-range strategy improved by 37% the penetration capabilities of an 80 kVp micro-CT imaging system for a total x-ray path length of 19.8 mm. Finally, our novel anti-scatter grid provided a 65% improvement in CT number accuracy and a 48% improvement in low-contrast visualization. Our proposed cost-effective scanner and artifact reduction strategies have the potential to improve patient care by accelerating the widespread use of patient-specific, bio-compatible, AM-manufactured, medical components

MRI-based radiomics: Quantifying the stability and reproducibility of tumour heterogeneity in vivo and in a 3D printed phantom

Magnetic resonance imaging (MRI) is a key component in the oncology workflow. Radiomics analysis is a new approach that uses standard of care (SOC) magnetic resonance (MR) images to non-invasively characterise tumour heterogeneity. For radiomics to be reliable, the imaging features measured must be stable and reproducible. This thesis aims to quantify the stability and reproducibility of MRI-based radiomics in vivo and in a 3D printed phantom. Chapter 4 explores the feasibility of constructing a 3D printed phantom using an MRI visible material (‘red resin’). The study shows that the material used to construct an anthropomorphic skull phantom mimicked human cortical bone with a T2* of 411 ± 19 µs. The phantom material provided sufficient signal for tissue segmentation however was only visible with an ultrashort echo time sequence, not commonly used in SOC imaging. Chapter 5 investigates a high temperature resin (‘white resin’) where a texture object was developed for analysis. The ‘white resin’ was visible using SOC sequences. The interscanner repeatability measurements of the texture phantom demonstrated high reproducibility with 76% of texture features having an ICC > 0.9. In chapter 6, further texture and shape objects were developed and employed in a multi-centre study assessing inter and intrascanner variation of MRI-based radiomics. The phantom was stable over a period of 12 months, with a T1 and T2 of 150.7 ± 6.7 ms and 56.1 ± 3.9 ms, respectively. The study also found that histogram features were more stable (ICC > 0.8 for 67%) compared to texture (ICC > 0.8 for 58%) and shape texture (ICC > 0.8 for 0%) across the 8 scanners. In chapter 7, phantom measurements found that radiomics features were more sensitive to changes of image resolution and noise. The in vivo test-retest component of chapter 7 detected many unstable features not suitable for use in a radiomics prognostic model. In chapter 8, of the 83 features computed only 19 features had significant changes between the baseline, mid and post radiation treatment and may be informative to assess rectal cancer treatment response. When considering using radiomics analysis for SOC MRI scans, caution must be taken to ensure imaging protocols, imaging equipment including scanners and coils are consistent to improve intra and inter-institutional feature robustness. This can be achieved with regular quality assurance (QA) of imaging protocols using a suitable phantom and appropriate feature selection using phantom and in vivo datasets

Ultra-High Field Strength MR Image-Guided Robotic Needle Delivery Device for In-Bore Small Animal Interventions

Current methods of accurate soft tissue injections in small animals are prone to many sources of error. Although efforts have been made to improve the accuracy of needle deliveries, none of the efforts have provided accurate soft tissue references. An MR image-guided robot was designed to function inside the bore of a 9.4T MR scanner to accurately deliver needles to locations within the mouse brain. The robot was designed to have no noticeable negative effects on the image quality and was localized in the MR images through the use of an MR image visible fiducial. The robot was mechanically calibrated and subsequently validated in an image-guided phantom experiment, where the mean needle targeting accuracy and needle trajectory accuracy were calculated to be 178 ± 54µm and 0.27 ± 0.65º, respectively. Finally, the device successfully demonstrated an image-guided needle targeting procedure in situ

Systematic review of pre-clinical and clinical devices for magnetic resonance-guided radiofrequency hyperthermia

Clinical trials have demonstrated the therapeutic benefits of adding radiofrequency (RF) hyperthermia (HT) as an adjuvant to radio- and chemotherapy. However, maximum utilization of these benefits is hampered by the current inability to maintain the temperature within the desired range. RF HT treatment quality is usually monitored by invasive temperature sensors, which provide limited data sampling and are prone to infection risks. Magnetic resonance (MR) temperature imaging has been developed to overcome these hurdles by allowing noninvasive 3D temperature monitoring in the target and normal tissues. To exploit this feature, several approaches for inserting the RF heating devices into the MR scanner have been proposed over the years. In this review, we summarize the status quo in MR-guided RF HT devices and analyze trends in these hybrid hardware configurations. In addition, we discuss the various approaches, extract best practices and identify gaps regarding the experimental validation procedures for MR - RF HT, aimed at converging to a common standard in this process