Slice Selection Research Articles

Automatic Best Reference Slice Selection for Smooth Volume Reconstruction of a Mouse Brain From Histological Images

In this paper, we present a novel and effective method for registering histological slices of a mouse brain to reconstruct a 3-D volume. First, intensity variations in images are corrected through an intensity standardization process so that intensity values remain constant across slices. Second, the image space is transformed to a feature space where continuous variables are taken as high fidelity image features for accurate registration. Third, in order to improve the quality of the reconstructed volume, an automatic best reference slice selection algorithm is developed based on iterative assessment of image entropy and mean square error of the registration process. Fourth, a novel metric for evaluating the quality of the reconstructed volume is developed. Finally, the effect of optimal reference slice selection on the quality of registration and subsequent reconstruction is demonstrated.

WE‐C‐204B‐07: Real‐Time MRI for Soft‐Tissue‐Based IGRT of Moving and Deforming Lung Tumors

Purpose: Integrated MRI+Linacs can potentially provide real‐time soft‐tissue‐based image‐guidance for lung cancer IGRT. Towards this, we investigate guidance strategies using prospective rapid lung MRI coupled with deformable image registration. Method and Materials: All experiments were performed on a 1.5 T MRI scanner, using a 4‐channel cardiac coil, under free‐breathing conditions, without extrinisic contrast. A balanced steady‐state free precession (b‐SSFP) imaging sequence was optimized for prospective imaging and reconstruction. Two lung cancer patients (Pt#l: 4 cm tumor, right lower lobe, Pt#2: 6 cm tumor, left upper lobe) were imaged. A viscous fluid‐flow‐based deformable registration was applied to each MRI time series in order to determine motion trajectories of voxels within the field of view. These trajectories were used to characterize:(i) motion of the tumor centroid.(ii) relative trajectories of the tumor centroid and the diaphragmrelative trajectories of different points on the tumor — characterizing tumor rotation/deformation.Results: The modified b‐SSFP sequence yielded acquisition times of ∼0.16s and ∼1.5s for 2D and 3D acquisition, respectively.Tumor trajectory analysis:(i) significant cycle‐to‐cycle variation in tumor motion was observed in both patients(ii) For Pt#l, the tumor centroid showed good correlation with diaphragmatic motion. For Pt#2, this correlation was relatively poor(iii) Pt#l did not exhibit significant tumor rotation/deformation. In Pt.#2, the trajectories of two points on the tumor showed maximum deviations of ∼8 mm (superior‐inferior) and 3.4 mm (anterior‐posterior), indicating non‐negligible rotation/deformation likely due to the influence of the adjacent cardiac wall.Conclusion: To our knowledge, this is the first demonstration of MRI for real‐time imaging of lung cancer. The incorporation of these strategies into MRI+Linacs offers image‐guidance capabilities that are not possible using current techniques: (i) soft‐tissue‐based rather than surrogate‐based monitoring (ii) no fiducial implantation or imaging dose (iii) arbitrary slice selection and (iv) ability to monitor complex motion.

Consequences of T2 relaxation during half‐pulse slice selection for ultrashort TE imaging

A "half-pulse" slice selection approach is used in the ultrashort echo time pulse sequence and is required to give minimal transverse relaxation in a two-dimensional acquisition. This method splits the normal excitation radiofrequency pulse in half and acquires a pair of images, each using one of these half-pulses. These half-pulses are used without a refocusing gradient since summing the pair of images yields images with accurate slice selection. When the radiofrequency pulse duration is similar to the sample T(2), characteristics such as the effective echo time and choice of radiofrequency pulse require careful evaluation as some of the approximations in conventional slice selection do not apply. We derive a theory that includes relaxation during excitation using Pauly's excitation k-space formalism. Further, this theory is tested on phantoms with a range of values of T(2) demonstrating the effect on the slice profile. We conclude that relaxation during excitation is significant and should be included in our estimate of the T(2) weighting of the sequence. In general, the T(2) weighting should be measured from the time of the centroid of the excitation pulse.

A comparison of radiographers and radiologists in CT based measurements of abdominal aortic aneurysms

Aim To evaluate the variability of CT AAA measurements undertaken by radiologists and radiographers. Methods 19 Observers (4 radiologists, 15 radiographers) were invited to independently measure maximum aneurysm diameter (Dmax) on ten CT scans. Each CT scan was presented randomly to each observer; four were duplicates testing intra-observer variability. All measurements were undertaken from axial CT images using electronic callipers, all observers were blinded to any previous measurements. Both the slice number and the maximum AAA diameter (in any plane) were recorded. Results Intra-observer variability was lower for radiographers with a mean paired difference of −0.18 ± 2.6 mm compared to −2.1 ± 3.5 mm ( P = 0.054). Inter-observer variability within each observer group was comparable, radiographers 0.1 ± 5.0 mm; radiologists −0.1 ± 3.1 mm ( P = 0.680). When directly comparing between the two groups mean difference was −2.0 ± 4.0 mm with 43% of paired measurements ≤2 mm or less and 78% ≤5 mm. Slice selection was less variable between the two groups with 88% of repeat radiographer measurements within ±1 slice and 91% of radiologists measurements with ±1 slice ( P = 0.228). Conclusion The accuracy of radiographers in performing AAA CT measurements is encouraging. Variability exists for both professions, and in some instances may be clinically significant. Observers should be aware of measurement variability issues and have an understanding of the factors responsible. Careful and repeat measurements of AAAs around 5.5 cm are recommended in order to define treatment.

New measures for estimating surface complementarity and packing at protein–protein interfaces

A number of methods exist that use different approaches to assess geometric properties like the surface complementarity and atom packing at the protein–protein interface. We have developed two new and conceptually different measures using the Delaunay tessellation and interface slice selection to compute the surface complementarity and atom packing at the protein–protein interface in a straightforward manner. Our measures show a strong correlation among themselves and with other existing measures, and can be calculated in a highly time-efficient manner. The measures are discriminative for evaluating biological, as well as non-biological protein–protein contacts, especially from large protein complexes and large-scale structural studies (http://pallab.serc.iisc.ernet.in/nip_nsc).

Padronização de um método para mensuração das tábuas ósseas vestibular e lingual dos maxilares na Tomografia Computadorizada de Feixe Cônico (Cone Beam)

INTRODUÇÃO: a espessura das tábuas ósseas que recobrem os dentes por vestibular e lingual constitui um dos fatores limitantes da movimentação dentária. O avanço tecnológico em Imaginologia permitiu avaliar detalhadamente essas regiões anatômicas por meio da utilização da tomografia computadorizada de feixe cônico (TCFC). OBJETIVO: descrever e padronizar, pormenorizadamente, um método para mensuração das tábuas ósseas vestibular e lingual dos maxilares nas imagens de tomografia computadorizada de feixe cônico. METODOLOGIA: a padronização digital da posição da imagem da face deve constituir o primeiro passo antes da seleção dos cortes de TCFC. Dois cortes axiais de cada maxilar foram empregados para a mensuração da espessura do osso alveolar vestibular e lingual. Utilizou-se como referência a junção cemento-esmalte dos primeiros molares permanentes, tanto na arcada superior quanto na inferior. RESULTADOS: cortes axiais paralelos ao plano palatino foram indicados para avaliação quantitativa do osso alveolar na maxila. Na arcada inferior, os cortes axiais devem ser paralelos ao plano oclusal funcional. CONCLUSÃO: o método descrito apresenta reprodutibilidade para utilização em pesquisas, assim como para a avaliação clínica das repercussões periodontais da movimentação dentária, ao permitir a comparação de imagens pré e pós-tratamento.

Self-refocused slice selection by magic echo DANTE with 270° flipping Gaussian RF modulation

The method of slice selection proposed for solid-state MRI by combining DANTE selective excitation with magic echo (ME) line narrowing requires a rephasing period ca. 0.6 times the DANTE excitation period. The added rephasing period results in a significant loss of sensitivity due to transverse relaxation. To solve the sensitivity problem, we make use of the self-refocusing effect of the 270° Gaussian-shaped soft pulse by introducing a 270° flipping Gaussian modulation to the ME DANTE method. This eliminates the rephasing period. The utility of the improved method is demonstrated by experiments performed on test samples of adamantane and polycarbonate.

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A magnetic resonance imaging (MRI) system compatible linear stage was developed. The stage was made of acrylic plastic and moving power was applied by an ultrasonic motor. Moving distance of the stage was detected by counting the number of motor rotations using a optic fiber sensor. Accuracy and precision of the stage control were measured inside and outside the magnet using a micrometer and a laser distance meter. As a result, a value of more than 95% was achieved in both of them in the 1.5 T magnetic field when it was applied for more than a 0.3 mm movement. Measurement of the slice sensitivity profile (SSP) by the delta method was performed. Slice selection by this linear stage and by radio frequency (RF) offset were compared. The result by linear stage was in good agreement with the result by RF offset. With this linear stage, a performance evaluation test of MRI equipments that need micromotion can be performed.

Evaluation of the clinical staging of esophageal cancer by using diffusion-weighted imaging

The purpose of this study was to assess the effectiveness of the apparent diffusion coefficient (ADC) using diffusion-weighted imaging (DWI) for the clinical staging of esophageal cancer. The ADC of the tumors was compared to the standardized uptake value (SUV) of 18F-fluorodeoxyglucose-positron emission tomography (FDG-PET). A total of 123 consecutive patients with esophageal squamous cell cancer were enrolled. DW images were obtained using a 1.5T whole-body scanner equipped with a phased-array body coil. A single shot spin-echo type of echo-planar sequence that provided diffusion weighting in the direction of the slice selection was used to obtain DW images. There was a negative correlation between the ADC value of the tumors and tumor diameter. A negative correlation was also found between the ADC value/SUV of the FDG-PET and serum levels of the tumor markers squamous cell carcinoma antigen and CYFRA. The ADC value was significantly correlated with clinical T and N stages. The ADC values of advanced-stage tumors were significantly lower than those of early-stage tumors. The ADC value of esophageal cancer decreased as the clinical stage advanced, and was correlated with the clinical findings. This non-invasive modality may be a valid clinical imaging method for the staging of esophageal cancer.

Small field of view imaging using wavelet encoding with 2 dimensional RF pulses and gradient echo: phantom results

The objective of this work is to propose an imaging sequence based upon the wavelet encoding approach to provide MRI images free from folding artifacts, in the small field of view (FOV) regime, such as dynamic magnetic resonance imaging (MRI) studies. The method consists of using a 2D spatially selective RF excitation pulse inserted into a gradient- echo pulse sequence to excite spins within a determined plane where wavelet encoding is achieved in one direction and slice selection is performed in the second direction. Wavelet encoding allows for spatially localized excitation and consequently restricts the spins excited within a reduced FOV. It consists of varying, according to a predetermined scheme, the width and position of the profile of the so-called fast RF pulse of the 2D RF excitation pulse, to obey wavelet encoding translation and dilation conditions. This sequence is implemented on a 3 Tesla whole body Siemens scanner. Compared to Fourier encoding, the proposed technique tested on phantoms with different shapes and structures, is able to provide gradient-echo reduced FOV images free from aliased signals. Wavelet encoding is suitable for small FOV imaging in dynamic MRI studies.

Slice profile effects in 2D slice-selective MRI of hyperpolarized nuclei

This work explores slice profile effects in 2D slice-selective gradient-echo MRI of hyperpolarized nuclei. Two different sequences were investigated: a Spoiled Gradient Echo sequence with variable flip angle (SPGR-VFA) and a balanced Steady-State Free Precession (SSFP) sequence. It is shown that in SPGR-VFA the distribution of flip angles across the slice present in any realistically shaped radiofrequency (RF) pulse leads to large excess signal from the slice edges in later RF views, which results in an undesired non-constant total transverse magnetization, potentially exceeding the initial value by almost 300% for the last RF pulse. A method to reduce this unwanted effect is demonstrated, based on dynamic scaling of the slice selection gradient. SSFP sequences with small to moderate flip angles (<40 degrees ) are also shown to preserve the slice profile better than the most commonly used SPGR sequence with constant flip angle (SPGR-CFA). For higher flip angles, the slice profile in SSFP evolves in a manner similar to SPGR-CFA, with depletion of polarization in the center of the slice.

MRI using radiofrequency magnetic field phase gradients

Conventionally, MR images are formed by applying gradients to the main static magnetic field (B0). However, the B0 gradient equipment is expensive, power-hungry, complex, and noisy and can induce eddy currents in nearby conducting structures, including the patient. Here, we describe a new silent, B0 gradient-free MRI principle, Transmit Array Spatial Encoding (TRASE), based on phase gradients of the radio-frequency (RF) field. RF phase gradients offer a new method of k-space traversal. Echo trains using at least two different RF phase gradients allow spin phase to accumulate, causing k-space traversal. Two such RF fields provide one-dimensional imaging and three are sufficient for two-dimensional imaging. Since TRASE is a k-space method, analogues of many conventional pulse sequences are possible. Experimental results demonstrate one-dimensional and two-dimensional RF MRI and slice selection using a single-channel, transmit/receive, 0.2 T, permanent magnet, human MR system. The experimentally demonstrated spatial resolution is much higher than that provided by RF receive coil array sensitivity encoding alone but lower than generally achievable with B0 gradients. Potential applications are those in which one or more of the features of simplified equipment, lower costs, silent MRI, or the different physics of the image formation process are particularly advantageous.

Detection of lactate with a hadamard slice selected, selective multiple quantum coherence, chemical shift imaging sequence (HDMD‐SelMQC‐CSI) on a clinical MRI scanner: Application to tumors and muscle ischemia

Lactate is an important metabolite in normal and malignant tissues detectable by NMR spectroscopy; however, it has been difficult to clinically detect the lactate methyl resonance because it is obscured by lipid resonances. The selective homonuclear multiple quantum coherence transfer technique offers a method for distinguishing lipid and lactate resonances. We implemented a three-dimensional selective homonuclear multiple quantum coherence transfer version with Hadamard slice selection and two-dimensional phase encoding (Hadamard encoded-selective homonuclear multiple quantum coherence transfer-chemical shift imaging) on a conventional clinical MR scanner. Hadamard slice selection is explained and demonstrated in vivo. This is followed by 1-cm(3) resolution lactate imaging with detection to 5-mM concentration in 20 min on a 3-T clinical scanner. An analysis of QSel gradient duration and amplitude effects on lactate and lipid signal is presented. To demonstrate clinical feasibility, a 5-min lactate scan of a patient with a non-Hodgkin's lymphoma in the superficial thigh is reported. The elevated lactate signal coincides with the T(2)-weighted image of this tumor. As a test of selective homonuclear multiple quantum coherence transfer sensitivity, a thigh tourniquet was applied to a normal volunteer and an increase in lactate was detected immediately after tourniquet flow constriction. In conclusion, the Hadamard encoded-selective homonuclear multiple quantum coherence transfer-chemical shift imaging sequence is demonstrated on a phantom and in two lipid-rich, clinically relevant, in vivo conditions.

Effect of slice angle on inhomogeneity artifact and its correction in slice‐selective MR imaging

AbstractThe inhomogeneity of a local magnetic field causes an image artifact of geometric distortion and intensity abnormality because of the slice offset and readout shift in slice‐selective MR imaging. It has been found that this artifact can be corrected by the projection of the slice offset onto the readout axis at a certain oblique slice angle. The slice angle for the artifact correction is determined by the amplitude of slice selection and readout gradients, and is independent of the magnetic field inhomogeneity and the main magnetic field direction. In addition, the existing view‐angle tilting technique is found to be valid only for the slice orientation orthogonal to the object axis. The slice angle effect on the inhomogeneity artifact was confirmed experimentally through phantom and volunteer's head imaging for both regular and view‐angle tilted spin echo sequences at 3 T. © 2009 Wiley Periodicals, Inc.Concepts Magn Reson Part A 34A: 238–248, 2009.

Material Orientation Artifact Studies in Magnetic Resonance Imaging

With the increased interest of MRI guided interventional procedures in modern medical treatments, image distortion and artifact formation based on material selection and orientation within the MRI scanner are central concerns for precise object localization. The goal of this study was to illustrate the artifact behavior of materials with various magnetic susceptibilities and radio frequency conductivity values corresponding to object orientation relative to the primary magnetic field. To test the effects of orientation on image distortion and image artifacts, 0.125 inch cylindrical test samples of various materials were imaged using a clinical Siemens 3 Tesla MR scanner. Modern medical instrumentation and surgical utensils are typically made from highly paramagnetic materials (e.g., titanium, nitinol, or stainless steel) which also have high RF conductivities. The combination of these two material properties cause both primary magnetic field (B0) and RF field (B1) inhomogeneities which lead to local image distortions. A change in the local magnetic field induces errors within the slice selection gradient, as the precessional frequency of the proton nuclei in the desired region of interest will not correspond to the exact spatial location on the object and will excite a broader region due to the RF conductivity of the material. Conversely to more traditional surgical materials, diamagnetic materials (e.g., bismuth, pyrolytic carbon, water, most plastics) are free from the susceptibility artifacts due to B0 inhomogeneities and thus offer a level of MR compatibility that traditional materials cannot. A specific testing phantom was built to fit a clinical wrist coil. The phantom consisted of an aqueous solution of gadolinium and copper sulfate to increase image contrast and a rotatable turret post for sample positioning. The particular materials studied were chosen to demonstrate the wide variation in both magnetic susceptibility values and RF conductivities (e.g., 6A1-4V titanium, 316L stainless steel, carbon fiber, 6061 T6 aluminum, brass, copper, beryllium copper). ImageJ software measured the overall pixel area and major dimension of each MR image artifact at 0, 45, and 90 degree orientations of each test sample relative to B0. The results of the measurements indicated measurable increases in signal are of the paramagnetic and highly conductive test specimens orientated orthogonal to the primary magnetic field. For instance, two common medical grade materials such as 316L stainless steel and 6Al-4V titanium resulted in artifact area increases of 770±10% and 234±10%, respectively, relative to the actual cross sectional area of the sample. Conversely, the more diamagnetic materials, carbon fiber and beryllium copper demonstrated increased artifact areas of 8±10% and 12±10%, respectively. Errors in artifact area percentage growth measurement are primarily attributed to manual image segmentation and variation in coil positioning within the MRI bore. The results indicate that MR image artifact size and object distortion characteristics can be influenced by both material selection and object orientation relative to the primary magnetic field. In the interest of accurate navigation of image guided equipment and devices, interventional devices should be tested for image distortion in multiple orientations. This work is supported by MIMTeC, a National Science Foundation Industry University Collaborative Research Center and by NIH Grant P30 NS057091.

Self‐refocused spatial‐spectral pulse for positive contrast imaging of cells labeled with SPIO nanoparticles

MRI has been used extensively to noninvasively track the location of cells labeled with superparamagnetic iron-oxide nanoparticles (SPIOs) in vivo. Typically, SPIOs are employed as a negative contrast agent which makes it difficult to differentiate labeled cells from extraneous sources of inhomogeneity and actual voids in the image. As a result, several novel approaches have been put forth to obtain positive contrast from SPIOs. One technique proposed by Cunningham et al. utilizes spectrally selective pulses to excite and refocus spins in the vicinity of the SPIOs. Although the frequency selectivity of this technique provides effective positive contrast, the lack of slice selectivity results in interfering signal from sources of off-resonance outside the slice of interest. We have developed a self-refocused spatial-spectral (SR-SPSP) pulse to achieve slice-selective spin-echo imaging of off-resonant spins. Using a self-refocused pulse affords flexibility in echo-time selection since the spin echo may be placed at any time after the end of the pulse. The spatial selectivity achieved by the SR-SPSP RF pulse eliminates background signal from out-of-slice regions and reduces the on-resonant water suppression requirements. Phantom and in vivo data demonstrate that positive contrast and slice-selectivity are achieved using this novel RF pulse.

Renal Stone Detection Using Unenhanced Multidetector Row Computerized Tomography—Does Section Width Matter?

We determined the effect of reconstructed section width on sensitivity and specificity for detecting renal calculi using multidetector row computerized tomography. Three to 5 renal stones 2 to 4 mm in size were randomly placed into 14 human cadaveric kidneys and scanned by 16-row detector computerized tomography at 1.25 mm collimation and identical scanning parameters. After acquisition images were reconstructed with a section width of 1.25, 2.5, 3.75 and 5.0 mm, and reviewed independently by 2 blinded radiologists. Comparisons of sensitivity and specificity between different section widths were assessed with the McNemar test and Cochran's Q statistics. Specificity was not significantly affected by section width (94.6% to 97.7%). In contrast, sensitivity increased as stone size increased and as section width decreased. Sensitivity to detect all stones was 80.7%, 80.7%, 87.7% and 92.1% for 5.0, 3.75, 2.5 and 1.25 mm section widths, respectively. Interobserver agreement for stone detection was excellent (kappa 0.858). Although the 2.0 mm stone detection rate improved with thinner section widths (79.4% vs 52.9% for 1.25 vs 5.0 mm, p = 0.004), stones greater than 2.0 mm were similarly detected at different slice selections (p = 0.056 to 0.572). Independent of other scanning parameters reconstruction section width influences the ability to detect small renal calculi. It must be considered when creating computerized tomography protocols.

Improved half RF slice selectivity in the presence of eddy currents with out‐of‐slice saturation

Ultrashort echo time imaging with half RF pulse excitation is sensitive to eddy currents induced by the slice-select gradient that distorts the half pulse slice profile. This work demonstrates improvements in the half pulse profile by using spatial saturation on both sides of the imaged slice to suppress the out-of-slice magnetization. This effectively improves the selectivity of the half pulse excitation profile. A quadratic phase RF pulse with high bandwidth and selectivity was used to achieve a wide saturation band with sharp edges. Experimental results demonstrate substantially improved slice selectivity and R(2)* quantitation accuracy obtained with the out-of-slice saturation. This approach is effective in making short T(2) imaging and quantitation with half pulses less sensitive to eddy currents.

Spectral-spatial pulse design for through-plane phase precompensatory slice selection in T2*-weighted functional MRI.

T(2)*-weighted functional MR images suffer from signal loss artifacts caused by the magnetic susceptibility differences between air cavities and brain tissues. We propose a novel spectral-spatial pulse design that is slice-selective and capable of mitigating the signal loss. The two-dimensional spectral-spatial pulses create precompensatory phase variations that counteract through-plane dephasing, relying on the assumption that resonance frequency offset and through-plane field gradient are spatially correlated. The pulses can be precomputed before functional MRI experiments and used repeatedly for different slices in different subjects. Experiments with human subjects showed that the pulses were effective in slice selection and loss mitigation at different brain regions.

Double half RF pulses for reduced sensitivity to eddy currents in UTE imaging

Ultrashort echo time imaging with half RF pulse excitation is challenging as eddy currents induced by the slice-select gradient distort the half pulse slice profile. This work presents two pulses with T(2)-dependent slice profiles that are less sensitive to eddy currents. The double half pulse improves the slice selectivity for long T(2) components, while the inverted double half pulse suppresses the unwanted long T(2) signal. Thus, both approaches prevent imperfect cancellation of out-of-slice signal from contaminating the desired slice. Experimental results demonstrate substantially improved slice selectivity and R(2)* quantitation accuracy with these pulses. These pulses are effective in making short T(2) imaging and quantitation less sensitive to eddy currents and provide an alternative to time-consuming gradient characterization.