Air bubble artifact reduction in post-mortem whole-brain MRI: the influence of receiver bandwidth

2018 ◽  
Vol 60 (10) ◽  
pp. 1089-1092 ◽  
Author(s):  
Max Scheffler ◽  
Enrique Maturana ◽  
Rares Salomir ◽  
Sven Haller ◽  
Enikö Kövari
Keyword(s):  
Brain Mri ◽  
Artifact Reduction ◽  
Post Mortem ◽  
Whole Brain ◽  
Air Bubble ◽  
Receiver Bandwidth

scholarly journals Tensor Image Registration Library: Automated Non-Linear Registration of Sparsely Sampled Histological Specimens to Post-Mortem MRI of the Whole Human Brain

2019 ◽  
Author(s):  
Istvan N. Huszar ◽  
Menuka Pallebage-Gamarallage ◽  
Sean Foxley ◽  
Benjamin C. Tendler ◽  
Anna Leonte ◽  
...  
Keyword(s):  
Image Registration ◽  
Human Brain ◽  
Brain Mri ◽  
List Type ◽  
Post Mortem ◽  
Whole Brain ◽  
Registration Method ◽  
Volume Registration ◽  
Histological Images ◽  
Automated Registration

AbstractThere is a need to understand the histopathological basis of MRI signal characteristics in complex biological matter. Microstructural imaging holds promise for sensitive and specific indicators of the early stages of human neurodegeneration but requires validation against traditional histological markers before it can be reliably applied in the clinical setting. Validation relies on a precise and preferably automatic method to align MRI and histological images of the same tissue, which poses unique challenges compared to more conventional MRI-to-MRI registration.A customisable open-source platform, Tensor Image Registration Library (TIRL) is presented. Based on TIRL, a fully automated pipeline was implemented to align small stained histological images with dissection photographs of corresponding tissue blocks and coronal brain slices, and further with high-resolution (0.5 mm) whole-brain post-mortem MRI data. The pipeline performed three separate deformable registrations to achieve accurate mapping between whole-brain MRI and small-slide histology coordinates. The robustness and accuracy of the individual registration steps were evaluated using both simulated data and real-life images from 6 different anatomical locations of one post-mortem human brain.The automated registration method demonstrated sub-millimetre accuracy in all steps, robustness against tissue damage, and good reproducibility between experiments. The method also outperformed manual landmark-based slice-to-volume registration, also correcting for curvatures in the slicing plane. Due to the customisability of TIRL, the pipeline can be conveniently adapted for other research needs and is therefore suitable for the large-scale comparison of routinely collected histology and MRI data.HighlightsTIRL: new framework for prototyping bespoke image registration pipelinesPipeline for automated registration of small-slide histology to whole-brain MRISlice-to-volume registration accounting for through-plane deformationsNo need for serial histological sampling

scholarly journals Can post-mortem MRI be used as a proxy for in vivo? A case study

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Baayla D C Boon ◽  
Petra J W Pouwels ◽  
Laura E Jonkman ◽  
Matthijs J Keijzer ◽  
Paolo Preziosa ◽  
...  
Keyword(s):  
White Matter ◽  
Rating Scales ◽  
Brain Volume ◽  
Brain Mri ◽  
Post Mortem ◽  
Early Onset Alzheimer’S Disease ◽  
And Diffusion

Abstract Post-mortem in situ MRI has been used as an intermediate between brain histo(patho)logy and in vivo imaging. However, it is not known how comparable post-mortem in situ is to ante-mortem imaging. We report the unique situation of a patient with familial early-onset Alzheimer’s disease due to a PSEN1 mutation, who underwent ante-mortem brain MRI and post-mortem in situ imaging only 4 days apart. T1-weighted and diffusion MRI was performed at 3-Tesla at both time points. Visual atrophy rating scales, brain volume, cortical thickness and diffusion measures were derived from both scans and compared. Post-mortem visual atrophy scores decreased 0.5–1 point compared with ante-mortem, indicating an increase in brain volume. This was confirmed by quantitative analysis; showing a 27% decrease of ventricular and 7% increase of whole-brain volume. This increase was more pronounced in the cerebellum and supratentorial white matter than in grey matter. Furthermore, axial and radial diffusivity decreased up to 60% post-mortem whereas average fractional anisotropy of white matter increased approximately 10%. This unique case study shows that the process of dying affects several imaging markers. These changes need to be taken into account when interpreting post-mortem MRI to make inferences on the in vivo situation.

An 8/15-channel Tx/Rx head neck RF coil combination with region-specific B1+ shimming for whole-brain MRI focused on the cerebellum at 7T

2018 ◽  
Vol 80 (3) ◽  
pp. 1252-1265 ◽  
Author(s):  
Viktor Pfaffenrot ◽  
Sascha Brunheim ◽  
Stefan H. G. Rietsch ◽  
Peter J. Koopmans ◽  
Thomas M. Ernst ◽  
...  
Keyword(s):  
Brain Mri ◽  
Rf Coil ◽  
Whole Brain ◽  
Head Neck

scholarly journals Volumetric assessment and longitudinal changes of brain structures in formalinized Beagle brains

2021 ◽  
Author(s):  
Francesca Del Signore ◽  
Germain Arribarat ◽  
Leonardo Della Salda ◽  
Giovanni Mogicato ◽  
Alexandra Deviers ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Brain Mri ◽  
Brain Structures ◽  
Formalin Fixation ◽  
Post Mortem ◽  
Intrinsic Variability ◽  
Advanced Technique ◽  
Longitudinal Changes ◽  
Beagle Dog ◽  
Volumetric Assessment

AbstractHigh field MRI represents an advanced technique both for diagnostic and research purposes on animal models such as the Beagle dog. The increasing interest in non-invasive neuroscience, aging, and neuropathological research led to a need of reference values (in terms of volumetric assessment) for the typical brain structures involved and, nowadays, several canine brain MRI atlases have been provided. Since no reports are available regarding the measurements reproducibility and few information are available about formalin fixation effect on brain structures when applied to MRI segmentation, we assessed the segmentation variability of selected structures as a function of the operator (two operators segmented the same data) and their intrinsic variability within a sample of 11 Beagle dogs (9 females and 2 males, 1.6 ± 0.2 years). Then, we analyzed for one further Beagle dog (2 years old) the longitudinal changes in the brain segmentations of these structures corresponding four conditions: in vivo, post mortem (after euthanasia), ex vivo (brain extracted and studied after 1 month in formalin and after 11 months); all the MRI images were collected with a 3 T MRI scanner. Our findings suggest that the segmentation procedure can be considered overall reproducible since only slight statistical differences were detected, apart from the ventricles.Furthermore, in the post mortem/ ex vivo comparison, the majority of the structures showed a higher contrast leading to more reproducible segmentations across operators and a net increase of volume of the studied structures; this could be justified by the intrinsic relaxation time changes observed as a consequence of formalin fixation, that led to an improvement of brain structures visualization and then segmentation.To conclude, MRI based segmentation seems to be a useful and accurate tool that allows longitudinal studies, especially when applied to formalin fixed brains.

scholarly journals Developing formalin‐based fixative agents for post mortem brain MRI at 9.4 T

2021 ◽  
Author(s):  
Azadeh Nazemorroaya ◽  
Ali Aghaeifar ◽  
Thomas Shiozawa ◽  
Bernhard Hirt ◽  
Hildegard Schulz ◽  
...  
Keyword(s):  
Brain Mri ◽  
Post Mortem ◽  
Post Mortem Brain
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