Data parsing in mass spectrometry imaging using R Studio and Cardinal: A tutorial

Mass spectrometry imaging (MSI) has emerged as a rapidly expanding field in the MS community. The analysis of large spectral data is further complicated by the added spatial dimension of MSI. A plethora of resources exist for expert users to begin parsing MSI data in R, but there is a critical lack of guidance for absolute beginners. This tutorial is designed to serve as a one-stop guide to start using R with MSI data and describe the possibilities that data science can bring to MSI analysis.

Morphological changes after cranial fractionated photon radiotherapy: Localized loss of white matter and grey matter volume with increasing dose

PURPOSE

Numerous brain MR imaging studies have been performed to understand radiation-induced cognitive decline. However, many of them focus on a single region of interest, e.g. cerebral cortex or hippocampus. In this study, we use deformation-based morphometry (DBM) and voxel-based morphometry (VBM) to measure the morphological changes in patients receiving fractionated photon RT, and relate these to the dose. Additionally, we study tissue specific volume changes in white matter (WM), grey matter (GM), cerebrospinal fluid and total intracranial volume (TIV).

METHODS AND MATERIALS

From our database, we selected 28 patients with MRI of high quality available at baseline and 1 year after RT. Scans were rigidly registered to each other, and to the planning CT and dose file. We used DBM to study non-tissue-specific volumetric changes, and VBM to study volume loss in grey matter. Observed changes were then related to the applied radiation dose (in EQD2). Additionally, brain tissue was segmented into WM, GM and cerebrospinal fluid, and changes in these volumes and TIV were tested.

RESULTS

Performing DBM resulted in clusters of dose-dependent volume loss 1 year after RT seen throughout the brain. Both WM and GM were affected; within the latter both cerebral cortex and subcortical nuclei show volume loss. Volume loss rates ranging from 5.3 to 15.3%/30 Gy were seen in the cerebral cortical regions in which more than 40% of voxels were affected. In VBM, similar loss rates were seen in the cortex and nuclei. The total volume of WM and GM significantly decreased with rates of 5.8% and 2.1%, while TIV remained unchanged as expected.

CONCLUSIONS

Radiotherapy is associated with dose-dependent intracranial morphological changes throughout the entire brain. Therefore, we will consider to revise sparing of organs at risk based on future cognitive and neurofunctional data.

Recent developments on PET radiotracers for TSPO and their applications in neuroimaging

The 18 kDa translocator protein (TSPO), previously known as the peripheral benzodiazepine receptor, is predominately localized to the outer mitochondrial membrane in steroidogenic cells. Brain TSPO expression is relatively low under physiological conditions, but is upregulated in response to glial cell activation. As the primary index of neuroinflammation, TSPO is implicated in the pathogenesis and progression of numerous neuropsychiatric disorders and neurodegenerative diseases, including Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), Parkinson's disease (PD), multiple sclerosis (MS), major depressive disorder (MDD) and obsessive compulsive disorder (OCD). In this context, numerous TSPO-targeted positron emission tomography (PET) tracers have been developed. Among them, several radioligands have advanced to clinical research studies. In this review, we will overview the recent development of TSPO PET tracers, focusing on the radioligand design, radioisotope labeling, pharmacokinetics, and PET imaging evaluation. Additionally, we will consider current limitations, as well as translational potential for future application of TSPO radiopharmaceuticals. This review aims to not only present the challenges in current TSPO PET imaging, but to also provide a new perspective on TSPO targeted PET tracer discovery efforts. Addressing these challenges will facilitate the translation of TSPO in clinical studies of neuroinflammation associated with central nervous system diseases.

Dual energy imaging in cardiothoracic pathologies: A primer for radiologists and clinicians

Recent advances in dual-energy imaging techniques, dual-energy subtraction radiography (DESR) and dual-energy CT (DECT), offer new and useful additional information to conventional imaging, thus improving assessment of cardiothoracic abnormalities. DESR facilitates detection and characterization of pulmonary nodules. Other advantages of DESR include better depiction of pleural, lung parenchymal, airway and chest wall abnormalities, detection of foreign bodies and indwelling devices, improved visualization of cardiac and coronary artery calcifications helping in risk stratification of coronary artery disease, and diagnosing conditions like constrictive pericarditis and valvular stenosis. Commercially available DECT approaches are classified into emission based (dual rotation/spin, dual source, rapid kilovoltage switching and split beam) and detector-based (dual layer) systems. DECT provide several specialized image reconstructions. Virtual non-contrast images (VNC) allow for radiation dose reduction by obviating need for true non contrast images, low energy virtual mono-energetic images (VMI) boost contrast enhancement and help in salvaging otherwise non-diagnostic vascular studies, high energy VMI reduce beam hardening artifacts from metallic hardware or dense contrast material, and iodine density images allow quantitative and qualitative assessment of enhancement/iodine distribution. The large amount of data generated by DECT can affect interpreting physician efficiency but also limit clinical adoption of the technology. Optimization of the existing workflow and streamlining the integration between post-processing software and picture archiving and communication system (PACS) is therefore warranted.

Iterative reconstruction algorithm improves the image quality without affecting quantitative measurements of computed tomography perfusion in the upper abdomen

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Iterative image-reconstruction algorithm (ADMIRE) did not affect the quantitative measurements in CT perfusion.

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Iterative image-reconstruction algorithm (ADMIRE) did not affect the time attenuation curves in CT perfusion.

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Image noise was lower, but the SNR was higher, for iterative reconstructions in CT perfusion examinations with higher strength of noise reduction.

Objective

To investigate differences between reconstruction algorithms in quantitative perfusion values and time-attenuation curves in computed tomography perfusion (CTP) examinations of the upper abdomen.

Methods

Twenty-six CTP examinations were reconstructed with filtered back projection and an iterative reconstruction algorithm, advanced modeled iterative reconstruction (ADMIRE), with different levels of noise-reduction strength. Using the maximum-slope model, quantitative measurements were obtained: blood flow (mL/min/100 mL), blood volume (mL/100 mL), time to peak (s), arterial liver perfusion (mL/100 mL/min), portal venous liver perfusion (mL/100 mL/min), hepatic perfusion index (%), temporal maximum intensity projection (Hounsfield units (HU)) and temporal average HU. Time-attenuation curves for seven sites (left liver lobe, right liver lobe, hepatocellular carcinoma, spleen, gastric wall, pancreas, portal vein) were obtained. Mixed-model analysis was used for statistical evaluation. Image noise and the signal:noise ratio (SNR) were compared between four reconstructions, and statistical analysis of these reconstructions was made with a related-samples Friedman’s two-way analysis of variance by ranks test.

Results

There were no significant differences for quantitative measurements between the four reconstructions for all tissues. There were no significant differences between the AUC values of the time-attenuation curves between the four reconstructions for all tissues, including three automatic measurements (portal vein, aorta, spleen). There was a significant difference in image noise and SNR between the four reconstructions.

Conclusions

ADMIRE did not affect the quantitative measurements or time-attenuation curves of tissues in the upper abdomen. The image noise was lower, and the SNR higher, for iterative reconstructions with higher noise-reduction strengths.

Evaluation of striatonigral connectivity using probabilistic tractography in Parkinson's disease

The cardinal movement abnormalities of Parkinson's disease (PD), including tremor, muscle rigidity, and reduced speed and frequency of movements, are caused by degeneration of dopaminergic neurons in the substantia nigra that project to the putamen, compromising information flow through frontal-subcortical circuits. Typically, the nigrostriatal pathway is more severely affected on the side of the brain opposite (contralateral) to the side of the body that manifests initial symptoms. Several studies have suggested that PD is also associated with changes in white matter microstructural integrity. The goal of the present study was to further develop methods for measuring striatonigral connectivity differences between PD patients and age-matched controls using diffusion weighted magnetic resonance imaging (MRI).

In this cross-sectional study, 40 PD patients and 44 controls underwent diffusion weighted imaging (DWI) using a 40-direction MRI sequence as well as an optimized 60-direction sequence with overlapping slices. Regions of interest (ROIs) encompassing the putamen and substantia nigra were hand drawn in the space of the 40-direction data using high-contrast structural images and then coregistered to the 60-direction data. Probabilistic tractography was performed in the native space of each dataset by seeding the putamen ROI with an ipsilateral substantia nigra classification target. The effect of disease group (PD versus control) on mean putamen-SN connection probability and streamline density were then analyzed using generalized linear models controlling for age, gender, education, as well as seed and target region characteristics.

Mean putamen-SN streamline density was lower in PD on both sides of the brain and in both 40- and 60-direction data. The optimized sequence provided a greater separation between PD and control means; however, individual values overlapped between groups. The 60-direction data also yielded mean connection probability values either trending (ipsilateral) or significantly (contralateral) lower in the PD group. There were minor between-group differences in average diffusion measures within the substantia nigra ROIs that did not affect the results of the GLM analyses when included as covariates. Based on these results, we conclude that mean striatonigral structural connectivity differs between PD and control groups and that use of an optimized 60-direction DWI sequence with overlapping slices increases the sensitivity of the technique to putative disease-related differences. However, overlap in individual values between disease groups limits its use as a classifier.

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The nigrostriatal pathway degenerates in Parkinson's disease.

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Two diffusion tensor imaging (DTI) sequences were acquired in 84 participants.

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Structural connectivity between putamen and substantia nigra was quantified.

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Parkinson's patients had lower connection probability and streamline density.

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A 60-direction DTI sequence with overlapping slices was most sensitive.

Pathology of callosal damage in ALS: An ex-vivo, 7 T diffusion tensor MRI study

OBJECTIVES

The goal of this study was to better understand the changes in tissue microstructure that underlie white matter diffusion changes in ALS patients.

METHODS

Diffusion tensor imaging was carried out in postmortem brains of 4 ALS patients and two subjects without neurological disease on a 7 T MRI scanner using steady-state free precession sequences. Fractional anisotropy (FA) was measured in the genu, body, and splenium of the corpus callosum in formalin-fixed hemispheres. FA of the body and genu was expressed as ratio to FA of the splenium, a region unaffected in ALS. After imaging, tissue sections of the same segments of the callosum were stained for markers of different tissue components. Coded image fields were rated for pathological changes by blinded raters.

RESULTS

The FA body/FA splenium ratio was reduced in ALS patients compared to controls. Patchy areas of myelin pallor and cells immunostained for CD68, a microglial-macrophage marker, were only observed in the body of the callosum of ALS patients. Blinded ratings showed increased CD68 + microglial cells in the body of the corpus callosum in ALS patients, especially those with C9orf72 mutations, and increased reactive astrocytes throughout the callosum.

CONCLUSION

Reduced FA of the corpus callosum in ALS results from complex changes in tissue microstructure. Callosal segments with reduced FA had large numbers of microglia-macrophages in addition to loss of myelinated axons and astrogliosis. Microglial inflammation contributed to reduced FA in ALS, and may contribute to a pro-inflammatory state, but further work is needed to determine their role.

Perfusion magnetic resonance imaging provides additional information as compared to anatomical imaging for decision-making in vestibular schwannoma

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DSC/ASL-MRI can be acquired in growing VS with sufficient image quality.

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In most patients DSC and ASL techniques provide similar qualitative scores.

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These techniques can be of importance in future decision-making.

Objective

The added value of perfusion MRI for decision-making in vestibular schwannoma (VS) patients is unknown. MRI offers two perfusion methods: the first employing contrast agent (dynamic susceptibility contrast (DSC)-MRI) that provides information on cerebral blood volume (CBV) and cerebral blood flow (CBF), the second by magnetic labeling of blood (arterial spin labeling (ASL)-MRI), providing CBF-images. The goal of the current study is to investigate whether DSC and ASL perfusion MRI provides complimentary information to current anatomical imaging in treatment selection process of VS.

Methods

Nine patients with growing VS with extrameatal diameter >9 mm were included (>2 mm/year and 20% volume expansion/year) and one patient with 23 mm extrameatal VS without growth. DSC and ASL perfusion MRI were obtained on 3 T MRI. Perfusion in VS was scored as hyperintense, hypointense or isointense compared to the contralateral region.

Results

Seven patients showed hyperintense signal on DSC and ASL sequences. Three patients showed iso- or hypointense signal on at least one perfusion map (1 patient hypointense on both DSC-MRI and ASL; 1 patient isointense on DSC-CBF; 1 patient isointense on ASL). All patients showed enhancement on post-contrast T1 anatomical scan.

Conclusion

Perfusion MR provides additional information compared to anatomical imaging for decision-making in VS.

Visual assessment of biliary excretion of Gd-EOB-DTPA in patients with suspected diffuse liver disease - A biopsy-verified prospective study

OBJECTIVES

To qualitatively evaluate late dynamic contrast phases, 10, 20 and 30 min, after administration of Gd-EOB-DTPA with regard to biliary excretion in patients presenting with elevated liver enzymes without clinical signs of cirrhosis or hepatic decompensation and to compare the visual assessment of contrast agent excretion with histo-pathological fibrosis stage, contrast uptake parameters and blood tests.

METHODS

29 patients were prospectively examined using 1.5 T MRI. The visually assessed presence or absence of contrast agent for each of five anatomical regions in randomly reviewed time-series was summarized on a four grade scale for each patient. The scores, including a total visual score, were related to the histo-pathological findings, the quantitative contrast agent uptake parameters, expressed as K Hep or LSC_N, and blood tests.

RESULTS

No relationship between the fibrosis grade or contrast uptake parameters could be established. A negative correlation between the visual assessment and alkaline phosphatase (ALP) was found. Comparing a sub-group of cholestatic patients with fibrosis score and Gd-EOB-DTPA dynamic parameters did not add any additional significant correlation.

CONCLUSIONS

No correlation between visually assessed biliary excretion of Gd-EOB-DTPA and histo-pathological or contrast uptake parameters was found. A negative correlation between the visual assessment and alkaline phosphatase (ALP) was found.