21 research outputs found
Bundle-specific Tractogram Distribution Estimation Using Higher-order Streamline Differential Equation
Tractography traces the peak directions extracted from fiber orientation
distribution (FOD) suffering from ambiguous spatial correspondences between
diffusion directions and fiber geometry, which is prone to producing erroneous
tracks while missing true positive connections. The peaks-based tractography
methods 'locally' reconstructed streamlines in 'single to single' manner, thus
lacking of global information about the trend of the whole fiber bundle. In
this work, we propose a novel tractography method based on a bundle-specific
tractogram distribution function by using a higher-order streamline
differential equation, which reconstructs the streamline bundles in 'cluster to
cluster' manner. A unified framework for any higher-order streamline
differential equation is presented to describe the fiber bundles with disjoint
streamlines defined based on the diffusion tensor vector field. At the global
level, the tractography process is simplified as the estimation of
bundle-specific tractogram distribution (BTD) coefficients by minimizing the
energy optimization model, and is used to characterize the relations between
BTD and diffusion tensor vector under the prior guidance by introducing the
tractogram bundle information to provide anatomic priors. Experiments are
performed on simulated Hough, Sine, Circle data, ISMRM 2015 Tractography
Challenge data, FiberCup data, and in vivo data from the Human Connectome
Project (HCP) data for qualitative and quantitative evaluation. The results
demonstrate that our approach can reconstruct the complex global fiber bundles
directly. BTD reduces the error deviation and accumulation at the local level
and shows better results in reconstructing long-range, twisting, and large
fanning tracts
Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods
The corticospinal tract (CST) is a critically important white matter fiber
tract in the human brain that enables control of voluntary movements of the
body. Diffusion MRI tractography is the only method that enables the study of
the anatomy and variability of the CST pathway in human health. In this work,
we explored the performance of six widely used tractography methods for
reconstructing the CST and its somatotopic organization. We perform experiments
using diffusion MRI data from the Human Connectome Project. Four quantitative
measurements including reconstruction rate, the WM-GM interface coverage,
anatomical distribution of streamlines, and correlation with cortical volumes
to assess the advantages and limitations of each method. Overall, we conclude
that while current tractography methods have made progress toward the
well-known challenge of improving the reconstruction of the lateral projections
of the CST, the overall problem of performing a comprehensive CST
reconstruction, including clinically important projections in the lateral (hand
and face area) and medial portions (leg area), remains an important challenge
for diffusion MRI tractography.Comment: 41 pages, 19 figure
Reconstruction of the arcuate fasciculus for surgical planning in the setting of peritumoral edema using two-tensor unscented Kalman filter tractography
Background: Diffusion imaging tractography is increasingly used to trace critical fiber tracts in brain tumor patients to reduce the risk of post-operative neurological deficit. However, the effects of peritumoral edema pose a challenge to conventional tractography using the standard diffusion tensor model. The aim of this study was to present a novel technique using a two-tensor unscented Kalman filter (UKF) algorithm to track the arcuate fasciculus (AF) in brain tumor patients with peritumoral edema. Methods: Ten right-handed patients with left-sided brain tumors in the vicinity of language-related cortex and evidence of significant peritumoral edema were retrospectively selected for the study. All patients underwent 3-Tesla magnetic resonance imaging (MRI) including a diffusion-weighted dataset with 31 directions. Fiber tractography was performed using both single-tensor streamline and two-tensor UKF tractography. A two-regions-of-interest approach was applied to perform the delineation of the AF. Results from the two different tractography algorithms were compared visually and quantitatively. Results: Using single-tensor streamline tractography, the AF appeared disrupted in four patients and contained few fibers in the remaining six patients. Two-tensor UKF tractography delineated an AF that traversed edematous brain areas in all patients. The volume of the AF was significantly larger on two-tensor UKF than on single-tensor streamline tractography (p < 0.01). Conclusions: Two-tensor UKF tractography provides the ability to trace a larger volume AF than single-tensor streamline tractography in the setting of peritumoral edema in brain tumor patients
Edema-informed anatomically constrained particle filter tractography
International audienceIn this work, we propose an edema-informed anatomically constrained tractography paradigm that enables reconstructing larger spatial extent of white matter bundles as well as increased cortical coverage in the presence of edema. These improvements will help surgeons maximize the extent of the resection while minimizing the risk of cogni-tive deficits. The new paradigm is based on a segmentation of the brain into gray matter, white matter, corticospinal fluid, edema and tumor regions which utilizes a tumor growth model. Using this segmentation, a valid tracking domain is generated and, in combination with anatomically constrained particle filter tractography, allows streamlines to cross the edema region and reach the cortex. Using subjects with brain tumors, we show that our edema-informed anatomically constrained tractogra-phy paradigm increases the cortico-cortical connections that cross edema-contaminated regions when compared to traditional fractional anisotropy thresholded tracking
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Automated white matter fiber tract identification in patients with brain tumors
We propose a method for the automated identification of key white matter fiber tracts for neurosurgical planning, and we apply the method in a retrospective study of 18 consecutive neurosurgical patients with brain tumors. Our method is designed to be relatively robust to challenges in neurosurgical tractography, which include peritumoral edema, displacement, and mass effect caused by mass lesions. The proposed method has two parts. First, we learn a data-driven white matter parcellation or fiber cluster atlas using groupwise registration and spectral clustering of multi-fiber tractography from healthy controls. Key fiber tract clusters are identified in the atlas. Next, patient-specific fiber tracts are automatically identified using tractography-based registration to the atlas and spectral embedding of patient tractography. Results indicate good generalization of the data-driven atlas to patients: 80% of the 800 fiber clusters were identified in all 18 patients, and 94% of the 800 fiber clusters were found in 16 or more of the 18 patients. Automated subject-specific tract identification was evaluated by quantitative comparison to subject-specific motor and language functional MRI, focusing on the arcuate fasciculus (language) and corticospinal tracts (motor), which were identified in all patients. Results indicate good colocalization: 89 of 95, or 94%, of patient-specific language and motor activations were intersected by the corresponding identified tract. All patient-specific activations were within 3mm of the corresponding language or motor tract. Overall, our results indicate the potential of an automated method for identifying fiber tracts of interest for neurosurgical planning, even in patients with mass lesions
TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance
We propose a geometric deep-learning-based framework, TractGeoNet, for
performing regression using diffusion magnetic resonance imaging (dMRI)
tractography and associated pointwise tissue microstructure measurements. By
employing a point cloud representation, TractGeoNet can directly utilize
pointwise tissue microstructure and positional information from all points
within a fiber tract. To improve regression performance, we propose a novel
loss function, the Paired-Siamese Regression loss, which encourages the model
to focus on accurately predicting the relative differences between regression
label scores rather than just their absolute values. In addition, we propose a
Critical Region Localization algorithm to identify highly predictive anatomical
regions within the white matter fiber tracts for the regression task. We
evaluate the effectiveness of the proposed method by predicting individual
performance on two neuropsychological assessments of language using a dataset
of 20 association white matter fiber tracts from 806 subjects from the Human
Connectome Project. The results demonstrate superior prediction performance of
TractGeoNet compared to several popular regression models. Of the twenty tracts
studied, we find that the left arcuate fasciculus tract is the most highly
predictive of the two studied language performance assessments. The localized
critical regions are widespread and distributed across both hemispheres and all
cerebral lobes, including areas of the brain considered important for language
function such as superior and anterior temporal regions, pars opercularis, and
precentral gyrus. Overall, TractGeoNet demonstrates the potential of geometric
deep learning to enhance the study of the brain's white matter fiber tracts and
to relate their structure to human traits such as language performance.Comment: 28 pages, 7 figure
MR in vivo tractography for the reconstruction of cranial nerves course
Aim
The aim of my Ph.D. was to implement a diffusion tensor tractography (DTT) pipeline to reconstruct cranial nerve I (olfactory) to study COVID-19 patients, and anterior optic pathway (AOP, including optic nerve, chiasm, and optic tract) to study patients with sellar/parasellar tumors, and with Leber’s Hereditary Optic Neuropathy (LHON).
Methods
We recruited 23 patients with olfactory dysfunction after COVID-19 infection (mean age 37±14 years, 12 females); 27 patients with sellar/parasellar tumors displacing the optic chiasm eligible for endonasal endoscopic surgery (mean age 53. ±16.4 years, 13 female) and 6 LHON patients (mutation 11778/MT-ND4, mean age 24.9±15.7 years). Sex- and age-matched healthy control were also recruited.
In LHON patients, optical coherence tomography (OCT) was performed. Acquisitions were performed on a clinical high field 3-T MRI scanner, using a multi-shell HARDI (High Angular Resolution Diffusion Imaging) sequence (b-values 0-300-1000-2000 s/mm2, 64 maximum gradient directions, 2mm3 isotropic voxel). DTT was performed with a multi-tissue spherical deconvolution approach and mean diffusivity (MD) DTT metrics were compared with healthy controls using an unpaired t-test. Correlations of DTT metrics with clinical data were sought by regression analysis.
Results
In all 23 hypo/anosmic patients with previous COVID-19 infection the CN I was successfully reconstructed with no DTT metrics alterations, thus suggesting the pathogenetic role of central olfactory cortical system dysfunction.
In all 27 patients with sellar/parasellar tumors the AOP was reconstructed, and in 11/13 (84.7%) undergoing endonasal endoscopic surgery the anatomical fidelity of the reconstruction was confirmed; a significant decrease in MD within the chiasma (p<0.0001) was also found.
In LHON patients a reduction of MD in the AOP was significantly associated with OCT parameters (p=0.036).
Conclusions
Multi-shell HARDI diffusion-weighted MRI followed by multi-tissue spherical deconvolution for the DTT reconstruction of the CN I and AOP has been implemented, and its utility demonstrated in clinical practice