Arterial Spin Labelling MRI for non-invasive perfusion quantification in the brain and in the kidneys

Arterial spin labelling (ASL) magnetic resonance imaging allows completely non-invasive quantification of perfusion and is valuable for the evaluation of tissue function, activity, and viability. However, it has not yet been established in the clinical routine world-wide partly due to a lack of standardisation. This thesis aims to contribute to the transition of ASL into the clinical routine by investigating sources of variability in ASL-based perfusion quantification in the brain and in the kidneys. Firstly, quantification results obtained with different processing options and corrections or with different acquisition parameters were compared using synthetic data, data from healthy volunteers, and patient data. Differences in acquisition parameters and processing options used for analysis of brain ASL data resulted in significant differences in perfusion quantification. Secondly, synthetic ASL data sets of the kidneys mimicking in vivo acquisitions were generated. A data analysis pipeline was developed and evaluated using the synthetic data sets. The registration performed well for both kidneys, with mean structural similarity index measures increasing by 25% on average. The quantification yielded cortical and medullary perfusion values that agreed with a mean percentage difference of 21% and 16% for cortex and medulla, respectively, to the perfusion assumed for the generation of the synthetic data sets. Segmentation results from the processing pipeline agreed well with original segmentation masks, with Dice indices ranging 0.80-0.93, 0.78-0.89, and 0.64-0.84 for whole kidney, cortex, and medulla, respectively. Thirdly, kidney ASL data were acquired in healthy volunteers and analysed with the developed processing pipeline. Four ASL measurements were performed for each subject varying between free breathing or synchronised breathing and with or without cardiac triggering. Registration performed best when considering the entire image, with a 87% success rate and a mean duration of 30 minutes. Percentage differences between literature values and mean perfusion values were equal to or below 32%, 61%, and 53% for whole kidney, cortex, and medulla, respectively. Across subjects, perfusion values obtained for the four different measurements were only significantly different between the free breathing and synchronised breathing measurement when considering the whole left kidney. Temporal signal-to-noise ratio was not found to differ significantly between the four measurements. Renal perfusion was found to depend on the trigger delay chosen for cardiac triggering. This study’s results suggest that an acquisition in free breathing without cardiac triggering is the best choice for clinical applications

Implementation of clinically relevant and robust fMRI-based language lateralization: Choosing the laterality index calculation method.

The assessment of language lateralization has become widely used when planning neurosurgery close to language areas, due to individual specificities and potential influence of brain pathology. Functional magnetic resonance imaging (fMRI) allows non-invasive and quantitative assessment of language lateralization for presurgical planning using a laterality index (LI). However, the conventional method is limited by the dependence of the LI on the chosen activation threshold. To overcome this limitation, different threshold-independent LI calculations have been reported. The purpose of this study was to propose a simplified approach to threshold-independent LI calculation and compare it with three previously reported methods on the same cohort of subjects. Fifteen healthy subjects, who performed picture naming, verb generation, and word fluency tasks, were scanned. LI values were calculated for all subjects using four methods, and considering either the whole hemisphere or an atlas-defined language area. For each method, the subjects were ranked according to the calculated LI values, and the obtained rankings were compared. All LI calculation methods agreed in differentiating strong from weak lateralization on both hemispheric and regional scales (Spearman's correlation coefficients 0.59-1.00). In general, a more lateralized activation was found in the language area than in the whole hemisphere. The new method is well suited for application in the clinical practice as it is simple to implement, fast, and robust. The good agreement between LI calculation methods suggests that the choice of method is not key. Nevertheless, it should be consistent to allow a relative comparison of language lateralization between subjects

Synthetic Arterial Spin Labeling MRI of the Kidneys for Evaluation of Data Processing Pipeline

Accurate quantification of perfusion is crucial for diagnosis and monitoring of kidney function. Arterial spin labeling (ASL), a completely non-invasive magnetic resonance imaging technique, is a promising method for this application. However, differences in acquisition (e.g., ASL parameters, readout) and processing (e.g., registration, segmentation) between studies impede the comparison of results. To alleviate challenges arising solely from differences in processing pipelines, synthetic data are of great value. In this work, synthetic renal ASL data were generated using body models from the XCAT phantom and perfusion was added using the general kinetic model. Our in-house developed processing pipeline was then evaluated in terms of registration, quantification, and segmentation using the synthetic data. Registration performance was evaluated qualitatively with line profiles and quantitatively with mean structural similarity index measures (MSSIMs). Perfusion values obtained from the pipeline were compared to the values assumed when generating the synthetic data. Segmentation masks obtained by semi-automated procedure of the processing pipeline were compared to the original XCAT organ masks using the Dice index. Overall, the pipeline evaluation yielded good results. After registration, line profiles were smoother and, on average, MSSIMs increased by 25%. Mean perfusion values for cortex and medulla were close to the assumed perfusion of 250 mL/100 g/min and 50 mL/100 g/min, respectively. Dice indices ranged 0.80–0.93, 0.78–0.89, and 0.64–0.84 for whole kidney, cortex, and medulla, respectively. The generation of synthetic ASL data allows flexible choice of parameters and the generated data are well suited for evaluation of processing pipelines

Reproducibility of MRI-based white matter tract estimation using multi-fiber probabilistic tractography:effect of user-defined parameters and regions

OBJECTIVE: There is a pressing need to assess user-dependent reproducibility of multi-fibre probabilistic tractography in order to encourage clinical implementation of these advanced and relevant approaches. The goal of this study was to evaluate both intrinsic and inter-user reproducibility of corticospinal tract estimation. MATERIALS AND METHODS: Six clinical datasets including motor functional and diffusion MRI were used. Three users performed an independent tractography analysis following identical instructions. Dice indices were calculated to quantify the reproducibility of seed region, fMRI-based end region, and streamline maps. RESULTS: The inter-user reproducibility ranged 41–93%, 29–94%, and 50–92%, for seed regions, end regions, and streamline maps, respectively. Differences in streamline maps correlated with differences in seed and end regions. Good inter-user agreement in seed and end regions, yielded inter-user reproducibility close to the intrinsic reproducibility (92–97%) and in most cases higher than 80%. DISCUSSION: Uncertainties related to user-dependent decisions and the probabilistic nature of the analysis should be considered when interpreting probabilistic tractography data. The standardization of the methods used to define seed and end regions is a necessary step to improve the accuracy and robustness of multi-fiber probabilistic tractography in a clinical setting. Clinical users should choose a feasible compromise between reproducibility and analysis duration

Reproducibility of arterial spin labeling cerebral blood flow image processing: A report of the ISMRM open science initiative for perfusion imaging (OSIPI)_and the ASL MRI challenge.

Publication status: PublishedFunder: European Union; doi: http://dx.doi.org/10.13039/501100000780Funder: Netherlands Organisation for health Research and Development; doi: http://dx.doi.org/10.13039/501100001826Funder: ISMRM Perfusion Study GroupFunder: Netherlands Enterprise Agency; doi: http://dx.doi.org/10.13039/100013405Funder: EU Joint Program for Neurodegenerative Disease ResearchPURPOSE: Arterial spin labeling (ASL) is a widely used contrast-free MRI method for assessing cerebral blood flow (CBF). Despite the generally adopted ASL acquisition guidelines, there is still wide variability in ASL analysis. We explored this variability through the ISMRM-OSIPI ASL-MRI Challenge, aiming to establish best practices for more reproducible ASL analysis. METHODS: Eight teams analyzed the challenge data, which included a high-resolution T1-weighted anatomical image and 10 pseudo-continuous ASL datasets simulated using a digital reference object to generate ground-truth CBF values in normal and pathological states. We compared the accuracy of CBF quantification from each team's analysis to the ground truth across all voxels and within predefined brain regions. Reproducibility of CBF across analysis pipelines was assessed using the intra-class correlation coefficient (ICC), limits of agreement (LOA), and replicability of generating similar CBF estimates from different processing approaches. RESULTS: Absolute errors in CBF estimates compared to ground-truth synthetic data ranged from 18.36 to 48.12 mL/100 g/min. Realistic motion incorporated into three datasets produced the largest absolute error and variability between teams, with the least agreement (ICC and LOA) with ground-truth results. Fifty percent of the submissions were replicated, and one produced three times larger CBF errors (46.59 mL/100 g/min) compared to submitted results. CONCLUSIONS: Variability in CBF measurements, influenced by differences in image processing, especially to compensate for motion, highlights the significance of standardizing ASL analysis workflows. We provide a recommendation for ASL processing based on top-performing approaches as a step toward ASL standardization