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Chen NK, Bell RP, Meade CS. On the down-sampling of diffusion MRI data along the angular dimension. Magn Reson Imaging 2021; 82:104-110. [PMID: 34174330 PMCID: PMC8289744 DOI: 10.1016/j.mri.2021.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/23/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND It has been established that the diffusion gradient directions in diffusion MRI should be uniformly distributed in 3D spherical space, so that orientation-dependent diffusion properties (e.g., fractional anisotropy or FA) can be properly quantified. Sometimes the acquired data need to be down-sampled along the angular dimension before computing diffusion properties (e.g., to exclude data points corrupted by motion artifact; to harmonize data obtained with different protocols). It is important to quantitatively assess the impact of data down-sampling on measurement of diffusion properties. MATERIALS AND METHODS Here we report 1) a numerical procedure for down-sampling diffusion MRI (e.g., for data harmonization), and 2) a spatial uniformity index of diffusion directions, aiming to predict the quality of the chosen down-sampling schemes (e.g., from data harmonization; or rejection of motion corrupted data points). We quantitatively evaluated human diffusion MRI data, which were down-sampled from 64 or 60 diffusion gradient directions to 30 directions, in terms of their 1) FA value accuracy (using fully-sampled data as the ground truth), 2) FA fitting residuals, and 3) spatial uniformity indices. RESULTS Our experimental data show that the proposed spatial uniformity index is correlated with errors in FA obtained from down-sampled diffusion MRI data. The FA fitting residuals that are typically used to assess diffusion MRI quality are not correlated with either FA errors or spatial uniformity index. CONCLUSIONS These results suggest that the spatial uniformity index could be more valuable in assessing quality of down-sampled diffusion MRI data, as compared with FA fitting residual measures. We expect that our implemented software procedure should prove valuable for 1) guiding data harmonization for multi-site diffusion MRI studies, and 2) assessing the impact of rejecting motion corrupted data points on the accuracy of diffusion measures.
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Affiliation(s)
- Nan-Kuei Chen
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA.
| | - Ryan P Bell
- Department of Psychiatry & Behavioral Sciences, Duke University, Durham, NC, USA
| | - Christina S Meade
- Department of Psychiatry & Behavioral Sciences, Duke University, Durham, NC, USA
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Cruciata G. Editorial for "Optimal Diffusion Gradient Encoding Scheme for Diffusion Tensor Imaging Based on Golden Ratio". J Magn Reson Imaging 2021; 55:1582-1583. [PMID: 34596933 DOI: 10.1002/jmri.27946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Giuseppe Cruciata
- Division of Neuroradiology, Stony Brook University, HSC Level 4, Room 120, Stony Brook, New York, 11794-8460, USA
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Yang JYM, Beare R, Seal ML, Harvey AS, Anderson VA, Maixner WJ. A systematic evaluation of intraoperative white matter tract shift in pediatric epilepsy surgery using high-field MRI and probabilistic high angular resolution diffusion imaging tractography. J Neurosurg Pediatr 2017; 19:592-605. [PMID: 28304232 DOI: 10.3171/2016.11.peds16312] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Characterization of intraoperative white matter tract (WMT) shift has the potential to compensate for neuronavigation inaccuracies using preoperative brain imaging. This study aimed to quantify and characterize intraoperative WMT shift from the global hemispheric to the regional tract-based scale and to investigate the impact of intraoperative factors (IOFs). METHODS High angular resolution diffusion imaging (HARDI) diffusion-weighted data were acquired over 5 consecutive perioperative time points (MR1 to MR5) in 16 epilepsy patients (8 male; mean age 9.8 years, range 3.8-15.8 years) using diagnostic and intraoperative 3-T MRI scanners. MR1 was the preoperative planning scan. MR2 was the first intraoperative scan acquired with the patient's head fixed in the surgical position. MR3 was the second intraoperative scan acquired following craniotomy and durotomy, prior to lesion resection. MR4 was the last intraoperative scan acquired following lesion resection, prior to wound closure. MR5 was a postoperative scan acquired at the 3-month follow-up visit. Ten association WMT/WMT segments and 1 projection WMT were generated via a probabilistic tractography algorithm from each MRI scan. Image registration was performed through pairwise MRI alignments using the skull segmentation. The MR1 and MR2 pairing represented the first surgical stage. The MR2 and MR3 pairing represented the second surgical stage. The MR3 and MR4 (or MR5) pairing represented the third surgical stage. The WMT shift was quantified by measuring displacements between a pair of WMT centerlines. Linear mixed-effects regression analyses were carried out for 6 IOFs: head rotation, craniotomy size, durotomy size, resected lesion volume, presence of brain edema, and CSF loss via ventricular penetration. RESULTS The average WMT shift in the operative hemisphere was 2.37 mm (range 1.92-3.03 mm) during the first surgical stage, 2.19 mm (range 1.90-3.65 mm) during the second surgical stage, and 2.92 mm (range 2.19-4.32 mm) during the third surgical stage. Greater WMT shift occurred in the operative than the nonoperative hemisphere, in the WMTs adjacent to the surgical lesion rather than those remote to it, and in the superficial rather than the deep segment of the pyramidal tract. Durotomy size and resection size were significant, independent IOFs affecting WMT shift. The presence of brain edema was a marginally significant IOF. Craniotomy size, degree of head rotation, and ventricular penetration were not significant IOFs affecting WMT shift. CONCLUSIONS WMT shift occurs noticeably in tracts adjacent to the surgical lesions, and those motor tracts superficially placed in the operative hemisphere. Intraoperative probabilistic HARDI tractography following craniotomy, durotomy, and lesion resection may compensate for intraoperative WMT shift and improve neuronavigation accuracy.
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Affiliation(s)
| | - Richard Beare
- Developmental Imaging Group and.,Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Marc L Seal
- Developmental Imaging Group and.,Department of Paediatrics and
| | | | - Vicki A Anderson
- Psychology, Royal Children's Hospital.,Clinical Sciences Theme, Murdoch Childrens Research Institute.,Department of Paediatrics and.,School of Psychological Sciences, University of Melbourne; and
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Caiazzo G, Trojsi F, Cirillo M, Tedeschi G, Esposito F. Q-ball imaging models: comparison between high and low angular resolution diffusion-weighted MRI protocols for investigation of brain white matter integrity. Neuroradiology 2015; 58:209-15. [PMID: 26573606 DOI: 10.1007/s00234-015-1616-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/06/2015] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Q-ball imaging (QBI) is one of the typical data models for quantifying white matter (WM) anisotropy in diffusion-weighted MRI (DwMRI) studies. Brain and spinal investigation by high angular resolution DwMRI (high angular resolution imaging (HARDI)) protocols exhibits higher angular resolution in diffusion imaging compared to low angular resolution models, although with longer acquisition times. We aimed to assess the difference between QBI-derived anisotropy values from high and low angular resolution DwMRI protocols and their potential advantages or shortcomings in neuroradiology. METHODS Brain DwMRI data sets were acquired in seven healthy volunteers using both HARDI (b = 3000 s/mm(2), 54 gradient directions) and low angular resolution (b = 1000 s/mm(2), 32 gradient directions) acquisition schemes. For both sequences, tract of interest tractography and generalized fractional anisotropy (GFA) measures were extracted by using QBI model and were compared between the two data sets. RESULTS QBI tractography and voxel-wise analyses showed that some WM tracts, such as corpus callosum, inferior longitudinal, and uncinate fasciculi, were reconstructed as one-dominant-direction fiber bundles with both acquisition schemes. In these WM tracts, mean percent different difference in GFA between the two data sets was less than 5%. Contrariwise, multidirectional fiber bundles, such as corticospinal tract and superior longitudinal fasciculus, were more accurately depicted by HARDI acquisition scheme. CONCLUSION Our results suggest that the design of optimal DwMRI acquisition protocols for clinical investigation of WM anisotropy by QBI models should consider the specific brain target regions to be explored, inducing researchers to a trade-off choice between angular resolution and acquisition time.
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Affiliation(s)
- Giuseppina Caiazzo
- MRI Research Center SUN-FISM-Neurological Institute for Diagnosis and Care "Hermitage Capodimonte", Naples, Italy
- Department of Medical, Surgical, Neurological, Metabolic and Aging Sciences, Second University of Naples, Naples, Italy
| | - Francesca Trojsi
- MRI Research Center SUN-FISM-Neurological Institute for Diagnosis and Care "Hermitage Capodimonte", Naples, Italy
- Department of Medical, Surgical, Neurological, Metabolic and Aging Sciences, Second University of Naples, Naples, Italy
| | - Mario Cirillo
- MRI Research Center SUN-FISM-Neurological Institute for Diagnosis and Care "Hermitage Capodimonte", Naples, Italy
- Department of Medical, Surgical, Neurological, Metabolic and Aging Sciences, Second University of Naples, Naples, Italy
| | - Gioacchino Tedeschi
- MRI Research Center SUN-FISM-Neurological Institute for Diagnosis and Care "Hermitage Capodimonte", Naples, Italy
- Department of Medical, Surgical, Neurological, Metabolic and Aging Sciences, Second University of Naples, Naples, Italy
| | - Fabrizio Esposito
- Department of Medicine and Surgery, University of Salerno, Via Allende, 84081, Baronissi (Salerno), Italy.
- Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands.
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K-Optimal Gradient Encoding Scheme for Fourth-Order Tensor-Based Diffusion Profile Imaging. BIOMED RESEARCH INTERNATIONAL 2015; 2015:760230. [PMID: 26451376 PMCID: PMC4584248 DOI: 10.1155/2015/760230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/18/2022]
Abstract
The design of an optimal gradient encoding scheme (GES) is a fundamental problem in diffusion MRI. It is well studied for the case of second-order tensor imaging (Gaussian diffusion). However, it has not been investigated for the wide range of non-Gaussian diffusion models. The optimal GES is the one that minimizes the variance of the estimated parameters. Such a GES can be realized by minimizing the condition number of the design matrix (K-optimal design). In this paper, we propose a new approach to solve the K-optimal GES design problem for fourth-order tensor-based diffusion profile imaging. The problem is a nonconvex experiment design problem. Using convex relaxation, we reformulate it as a tractable semidefinite programming problem. Solving this problem leads to several theoretical properties of K-optimal design: (i) the odd moments of the K-optimal design must be zero; (ii) the even moments of the K-optimal design are proportional to the total number of measurements; (iii) the K-optimal design is not unique, in general; and (iv) the proposed method can be used to compute the K-optimal design for an arbitrary number of measurements. Our Monte Carlo simulations support the theoretical results and show that, in comparison with existing designs, the K-optimal design leads to the minimum signal deviation.
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Beltrachini L, von Ellenrieder N, Muravchik CH. Error bounds in diffusion tensor estimation using multiple-coil acquisition systems. Magn Reson Imaging 2013; 31:1372-83. [DOI: 10.1016/j.mri.2013.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 04/23/2013] [Accepted: 04/26/2013] [Indexed: 11/25/2022]
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Alipoor M, Gu IYH, Mehnert AJH, Lilja Y, Nilsson D. Optimal diffusion tensor imaging with repeated measurements. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2013; 16:687-694. [PMID: 24505727 DOI: 10.1007/978-3-642-40811-3_86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Several data acquisition schemes for diffusion MRI have been proposed and explored to date for the reconstruction of the 2nd order tensor. Our main contributions in this paper are: (i) the definition of a new class of sampling schemes based on repeated measurements in every sampling point; (ii) two novel schemes belonging to this class; and (iii) a new reconstruction framework for the second scheme. We also present an evaluation, based on Monte Carlo computer simulations, of the performances of these schemes relative to known optimal sampling schemes for both 2nd and 4th order tensors. The results demonstrate that tensor estimation by the proposed sampling schemes and estimation framework is more accurate and robust.
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Affiliation(s)
- Mohammad Alipoor
- Department of Signals and Systems, Chalmers University of Technology, Gothenburg, Sweden.
| | - Irene Yu Hua Gu
- Department of Signals and Systems, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew J H Mehnert
- Department of Signals and Systems, Chalmers University of Technology, Gothenburg, Sweden
| | - Ylva Lilja
- Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Daniel Nilsson
- Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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Tournier JD, Mori S, Leemans A. Diffusion tensor imaging and beyond. Magn Reson Med 2011; 65:1532-56. [PMID: 21469191 DOI: 10.1002/mrm.22924] [Citation(s) in RCA: 637] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 02/18/2011] [Indexed: 12/13/2022]
Affiliation(s)
- Jacques-Donald Tournier
- Brain Research Institute, Florey Neuroscience Institutes, Neurosciences Building, Austin Health, Heidelberg West, Victoria, Australia
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A review of diffusion tensor magnetic resonance imaging computational methods and software tools. Comput Biol Med 2010; 41:1062-72. [PMID: 21087766 DOI: 10.1016/j.compbiomed.2010.10.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/24/2010] [Accepted: 10/26/2010] [Indexed: 02/07/2023]
Abstract
In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided.
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Akkerman EM. The direct tensor solution and higher-order acquisition schemes for generalized diffusion tensor imaging. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 206:9-19. [PMID: 20579911 DOI: 10.1016/j.jmr.2010.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 05/17/2010] [Accepted: 05/17/2010] [Indexed: 05/29/2023]
Abstract
Both in diffusion tensor imaging (DTI) and in generalized diffusion tensor imaging (GDTI) the relation between the diffusion tensor and the measured apparent diffusion coefficients is given by a tensorial equation, which needs to be inverted in order to solve the diffusion tensor. The traditional way to do this does not preserve the tensorial structure of the equation, which we consider a weakness in the method. For a physically correct measurement procedure, the condition number of the acquisition scheme, which is a determinant of the noise behavior, needs to be rotationally invariant. The method which traditionally is used to find such schemes, however, is cumbersome and mathematically unsatisfactory. This is considered a second weakness, closely connected to the first. In this paper we present an alternative inversion of the diffusion tensor equation, which does preserve the tensor form, for arbitrary order, and which is named the direct tensor solution (DTS). The DTS is derived under the assumption that the apparent diffusion coefficient in any direction is known, i.e. in the infinite acquisition scheme. Whenever the DTS is valid for a given finite acquisition scheme and for a given order, the condition number is rotationally invariant. The DTS provides a compact, algebraic procedure to check this rotational invariance. We also present a method to construct acquisition schemes, for which the DTS is valid for the measurement of higher-order diffusion tensors. Furthermore, the DTS leads to other mathematical insights, such as tensorial relationships between diffusion tensors of different orders, and a more general understanding of the Platonic Variance Method, which we published before.
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Affiliation(s)
- Erik M Akkerman
- Department of Radiology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
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Liu C, Mang SC, Moseley ME. In vivo generalized diffusion tensor imaging (GDTI) using higher-order tensors (HOT). Magn Reson Med 2010; 63:243-52. [PMID: 19953513 DOI: 10.1002/mrm.22192] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Generalized diffusion tensor imaging (GDTI) using higher-order tensor (HOT) statistics generalizes the technique of diffusion tensor imaging by including the effect of nongaussian diffusion on the signal of MRI. In GDTI-HOT, the effect of nongaussian diffusion is characterized by higher-order tensor statistics (i.e., the cumulant tensors or the moment tensors), such as the covariance matrix (the second-order cumulant tensor), the skewness tensor (the third-order cumulant tensor), and the kurtosis tensor (the fourth-order cumulant tensor). Previously, Monte Carlo simulations have been applied to verify the validity of this technique in reconstructing complicated fiber structures. However, no in vivo implementation of GDTI-HOT has been reported. The primary goal of this study is to establish GDTI-HOT as a feasible in vivo technique for imaging nongaussian diffusion. We show that probability distribution function of the molecular diffusion process can be measured in vivo with GDTI-HOT and be visualized with three-dimensional glyphs. By comparing GDTI-HOT to fiber structures that are revealed by the highest resolution diffusion-weighted imaging (DWI) possible in vivo, we show that the GDTI-HOT can accurately predict multiple fiber orientations within one white matter voxel. Furthermore, through bootstrap analysis we demonstrate that in vivo measurement of HOT elements is reproducible, with a small statistical variation that is similar to that of diffusion tensor imaging.
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Affiliation(s)
- Chunlei Liu
- Brain Imaging and Analysis Center, Duke University, Durham, North Carolina 27705, USA.
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