Contour tree connectivity and analysis of microstructures

The connectivity of microstructures is directly related to the physical properties of materials. Currently, the Euler number is the most popular measure of connectivity. It is an elegant topological invariant, however, it does not provide information about cavities or the proximities and sizes of objects. In this thesis, an alternative measure called contour tree connectivity (CTC) is developed and its applications for the analysis of microstructures are studied. CTC is derived from contour trees that are used in the first publication to represent complex binary images with simple graphs. By analyzing contour trees, CTC produces new connectivity information that is not provided by other approaches described in the literature. Contour tree representation of binary images and CTC can be computed for any dimensions of data and topology as explained in the second publication. Moreover, CTC is designed to be a scalar between 0 and 1, which makes it easy to use and understand. In this thesis, the use of CTC for analyzing microstructures is presented in two studies. In the first study, the microstructure of trabecular bone is analyzed in relation to its mechanical strength. In the second study, the relationship between microstructures and the fluid flow within materials are examined. The results from these studies show that CTC contributes to the understanding of how the structural properties of materials are linked to their physical properties. To conclude, with its unique properties, CTC complements the structural information provided by currently used measures. This makes it an important image analysis tool for the study of the microstructures of materials such as soil, paper, filters and food products as well as biomaterials and biological tissues

Identification of proprioceptive thalamocortical tracts in children : comparison of fMRI, MEG, and manual seeding of probabilistic tractography

Studying white matter connections with tractography is a promising approach to understand the development of different brain processes, such as proprioception. An emerging method is to use functional brain imaging to select the cortical seed points for tractography, which is considered to improve the functional relevance and validity of the studied connections. However, it is unknown whether different functional seeding methods affect the spatial and microstructural properties of the given white matter connection. Here, we compared functional magnetic resonance imaging, magnetoencephalography, and manual seeding of thalamocortical proprioceptive tracts for finger and ankle joints separately. We showed that all three seeding approaches resulted in robust thalamocortical tracts, even though there were significant differences in localization of the respective proprioceptive seed areas in the sensorimotor cortex, and in the microstructural properties of the obtained tracts. Our study shows that the selected functional or manual seeding approach might cause systematic biases to the studied thalamocortical tracts. This result may indicate that the obtained tracts represent different portions and features of the somatosensory system. Our findings highlight the challenges of studying proprioception in the developing brain and illustrate the need for using multimodal imaging to obtain a comprehensive view of the studied brain process.Peer reviewe

Machine learning-based prediction of motor status in glioma patients using diffusion MRI metrics along the corticospinal tract

Shams et al. report that glioma patients' motor status is predicted accurately by diffusion MRI metrics along the corticospinal tract based on support vector machine method, reaching an overall accuracy of 77%. They show that these metrics are more effective than demographic and clinical variables. Along tract statistics enables white matter characterization using various diffusion MRI metrics. These diffusion models reveal detailed insights into white matter microstructural changes with development, pathology and function. Here, we aim at assessing the clinical utility of diffusion MRI metrics along the corticospinal tract, investigating whether motor glioma patients can be classified with respect to their motor status. We retrospectively included 116 brain tumour patients suffering from either left or right supratentorial, unilateral World Health Organization Grades II, III and IV gliomas with a mean age of 53.51 +/- 16.32 years. Around 37% of patients presented with preoperative motor function deficits according to the Medical Research Council scale. At group level comparison, the highest non-overlapping diffusion MRI differences were detected in the superior portion of the tracts' profiles. Fractional anisotropy and fibre density decrease, apparent diffusion coefficient axial diffusivity and radial diffusivity increase. To predict motor deficits, we developed a method based on a support vector machine using histogram-based features of diffusion MRI tract profiles (e.g. mean, standard deviation, kurtosis and skewness), following a recursive feature elimination method. Our model achieved high performance (74% sensitivity, 75% specificity, 74% overall accuracy and 77% area under the curve). We found that apparent diffusion coefficient, fractional anisotropy and radial diffusivity contributed more than other features to the model. Incorporating the patient demographics and clinical features such as age, tumour World Health Organization grade, tumour location, gender and resting motor threshold did not affect the model's performance, revealing that these features were not as effective as microstructural measures. These results shed light on the potential patterns of tumour-related microstructural white matter changes in the prediction of functional deficits.Peer reviewe

Machine learning-based prediction of motor status in glioma patients using diffusion MRI metrics along the corticospinal tract

Shams et al. report that glioma patients' motor status is predicted accurately by diffusion MRI metrics along the corticospinal tract based on support vector machine method, reaching an overall accuracy of 77%. They show that these metrics are more effective than demographic and clinical variables.Along tract statistics enables white matter characterization using various diffusion MRI metrics. These diffusion models reveal detailed insights into white matter microstructural changes with development, pathology and function. Here, we aim at assessing the clinical utility of diffusion MRI metrics along the corticospinal tract, investigating whether motor glioma patients can be classified with respect to their motor status. We retrospectively included 116 brain tumour patients suffering from either left or right supratentorial, unilateral World Health Organization Grades II, III and IV gliomas with a mean age of 53.51 +/- 16.32 years. Around 37% of patients presented with preoperative motor function deficits according to the Medical Research Council scale. At group level comparison, the highest non-overlapping diffusion MRI differences were detected in the superior portion of the tracts' profiles. Fractional anisotropy and fibre density decrease, apparent diffusion coefficient axial diffusivity and radial diffusivity increase. To predict motor deficits, we developed a method based on a support vector machine using histogram-based features of diffusion MRI tract profiles (e.g. mean, standard deviation, kurtosis and skewness), following a recursive feature elimination method. Our model achieved high performance (74% sensitivity, 75% specificity, 74% overall accuracy and 77% area under the curve). We found that apparent diffusion coefficient, fractional anisotropy and radial diffusivity contributed more than other features to the model. Incorporating the patient demographics and clinical features such as age, tumour World Health Organization grade, tumour location, gender and resting motor threshold did not affect the model's performance, revealing that these features were not as effective as microstructural measures. These results shed light on the potential patterns of tumour-related microstructural white matter changes in the prediction of functional deficits

brainlife.io: a decentralized and open-source cloud platform to support neuroscience research

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants

Contour tree connectivity and analysis of microstructures

The connectivity of microstructures is directly related to the physical properties of materials. Currently, the Euler number is the most popular measure of connectivity. It is an elegant topological invariant, however, it does not provide information about cavities or the proximities and sizes of objects. In this thesis, an alternative measure called contour tree connectivity (CTC) is developed and its applications for the analysis of microstructures are studied. CTC is derived from contour trees that are used in the first publication to represent complex binary images with simple graphs. By analyzing contour trees, CTC produces new connectivity information that is not provided by other approaches described in the literature. Contour tree representation of binary images and CTC can be computed for any dimensions of data and topology as explained in the second publication. Moreover, CTC is designed to be a scalar between 0 and 1, which makes it easy to use and understand. In this thesis, the use of CTC for analyzing microstructures is presented in two studies. In the first study, the microstructure of trabecular bone is analyzed in relation to its mechanical strength. In the second study, the relationship between microstructures and the fluid flow within materials are examined. The results from these studies show that CTC contributes to the understanding of how the structural properties of materials are linked to their physical properties. To conclude, with its unique properties, CTC complements the structural information provided by currently used measures. This makes it an important image analysis tool for the study of the microstructures of materials such as soil, paper, filters and food products as well as biomaterials and biological tissues

Limb-specific thalamocortical tracts are impaired differently in hemiplegic and diplegic subtypes of cerebral palsy

Thalamocortical pathways are considered crucial in the sensorimotor functioning of children with cerebral palsy (CP). However, previous research has been limited by non-specific tractography seeding and the lack of comparison between different CP subtypes. We compared limb-specific thalamocortical tracts between children with hemiplegic (HP, N = 15) or diplegic (DP, N = 10) CP and typically developed peers (N = 19). The cortical seed-points for the upper and lower extremities were selected (i) manually based on anatomical landmarks or (ii) using functional magnetic resonance imaging (fMRI) activations following proprioceptive-limb stimulation. Correlations were investigated between tract structure (mean diffusivity, MD; fractional anisotropy, FA; apparent fiber density, AFD) and sensorimotor performance (hand skill and postural stability). Compared to controls, our results revealed increased MD in both upper and lower limb thalamocortical tracts in the non-dominant hemisphere in HP and bilaterally in DP subgroup. MD was strongly lateralized in participants with hemiplegia, while AFD seemed lateralized only in controls. fMRI-based tractography results were comparable. The correlation analysis indicated an association between the white matter structure and sensorimotor performance. These findings suggest distinct impairment of functionally relevant thalamocortical pathways in HP and DP subtypes. Thus, the organization of thalamocortical white matter tracts may offer valuable guidance for targeted, life-long rehabilitation in children with CP.peerReviewe

Detecting Corticospinal Tract Impairment in Tumor Patients With Fiber Density and Tensor-Based Metrics

Tumors infiltrating the motor system lead to significant disability, often caused by corticospinal tract injury. The delineation of the healthy-pathological white matter (WM) interface area, for which diffusion magnetic resonance imaging (dMRI) has shown promising potential, may improve treatment outcome. However, up to 90% of white matter (WM) voxels include multiple fiber populations, which cannot be correctly described with traditional metrics such as fractional anisotropy (FA) or apparent diffusion coefficient (ADC). Here, we used a novel fixel-based along-tract analysis consisting of constrained spherical deconvolution (CSD)-based probabilistic tractography and fixel-based apparent fiber density (FD), capable of identifying fiber orientation specific microstructural metrics. We addressed this novel methodology’s capability to detect corticospinal tract impairment. We measured and compared tractogram-related FD and traditional microstructural metrics bihemispherically in 65 patients with WHO grade III and IV gliomas infiltrating the motor system. The cortical tractogram seeds were based on motor maps derived by transcranial magnetic stimulation. We extracted 100 equally distributed cross-sections along each streamline of corticospinal tract (CST) for along-tract statistical analysis. Cross-sections were then analyzed to detect differences between healthy and pathological hemispheres. All metrics showed significant differences between healthy and pathologic hemispheres over the entire tract and between peritumoral segments. Peritumoral values were lower for FA and FD, but higher for ADC within the entire cohort. FD was more specific to tumor-induced changes in CST than ADC or FA, whereas ADC and FA showed higher sensitivity. The bihemispheric along-tract analysis provides an approach to detect subject-specific structural changes in healthy and pathological WM. In the current clinical dataset, the more complex FD metrics did not outperform FA and ADC in terms of describing corticospinal tract impairment.Peer Reviewe