Intensity-based 3D motion correction for cardiac MR images

Cardiac magnetic resonance (CMR) image acquisition requires subjects to hold their breath while 2D cine images are acquired. This process assumes that the heart remains in the same position across all slices. However, differences in breathhold positions or patient motion introduce 3D slice misalignments. In this work, we propose an algorithm that simultaneously aligns all SA and LA slices by maximizing the pair-wise intensity agreement between their intersections. Unlike previous works, our approach is formulated as a subject-specific optimization problem and requires no prior knowledge of the underlying anatomy. We quantitatively demonstrate that the proposed method is robust against a large range of rotations and translations by synthetically misaligning 10 motion-free datasets and aligning them back using the proposed method

MAD: Modality Agnostic Distance Measure for Image Registration

Multi-modal image registration is a crucial pre-processing step in many medical applications. However, it is a challenging task due to the complex intensity relationships between different imaging modalities, which can result in large discrepancy in image appearance. The success of multi-modal image registration, whether it is conventional or learning based, is predicated upon the choice of an appropriate distance (or similarity) measure. Particularly, deep learning registration algorithms lack in accuracy or even fail completely when attempting to register data from an "unseen" modality. In this work, we present Modality Agnostic Distance (MAD), a deep image distance}] measure that utilises random convolutions to learn the inherent geometry of the images while being robust to large appearance changes. Random convolutions are geometry-preserving modules which we use to simulate an infinite number of synthetic modalities alleviating the need for aligned paired data during training. We can therefore train MAD on a mono-modal dataset and successfully apply it to a multi-modal dataset. We demonstrate that not only can MAD affinely register multi-modal images successfully, but it has also a larger capture range than traditional measures such as Mutual Information and Normalised Gradient Fields

Denoising diffusion-based MRI to CT image translation enables automated spinal segmentation

Background: Automated segmentation of spinal magnetic resonance imaging (MRI) plays a vital role both scientifically and clinically. However, accurately delineating posterior spine structures is challenging. Methods: This retrospective study, approved by the ethical committee, involved translating T1-weighted and T2-weighted images into computed tomography (CT) images in a total of 263 pairs of CT/MR series. Landmark-based registration was performed to align image pairs. We compared two-dimensional (2D) paired - Pix2Pix, denoising diffusion implicit models (DDIM) image mode, DDIM noise mode - and unpaired (SynDiff, contrastive unpaired translation) image-to-image translation using "peak signal-to-noise ratio" as quality measure. A publicly available segmentation network segmented the synthesized CT datasets, and Dice similarity coefficients (DSC) were evaluated on in-house test sets and the "MRSpineSeg Challenge" volumes. The 2D findings were extended to three-dimensional (3D) Pix2Pix and DDIM. Results: 2D paired methods and SynDiff exhibited similar translation performance and DCS on paired data. DDIM image mode achieved the highest image quality. SynDiff, Pix2Pix, and DDIM image mode demonstrated similar DSC (0.77). For craniocaudal axis rotations, at least two landmarks per vertebra were required for registration. The 3D translation outperformed the 2D approach, resulting in improved DSC (0.80) and anatomically accurate segmentations with higher spatial resolution than that of the original MRI series. Conclusions: Two landmarks per vertebra registration enabled paired image-to-image translation from MRI to CT and outperformed all unpaired approaches. The 3D techniques provided anatomically correct segmentations, avoiding underprediction of small structures like the spinous process. Relevance statement: This study addresses the unresolved issue of translating spinal MRI to CT, making CT-based tools usable for MRI data. It generates whole spine segmentation, previously unavailable in MRI, a prerequisite for biomechanical modeling and feature extraction for clinical applications. Key points: • Unpaired image translation lacks in converting spine MRI to CT effectively. • Paired translation needs registration with two landmarks per vertebra at least. • Paired image-to-image enables segmentation transfer to other domains. • 3D translation enables super resolution from MRI to CT. • 3D translation prevents underprediction of small structures

Denoising diffusion-based MR to CT image translation enables whole spine vertebral segmentation in 2D and 3D without manual annotations

Background: Automated segmentation of spinal MR images plays a vital role both scientifically and clinically. However, accurately delineating posterior spine structures presents challenges. Methods: This retrospective study, approved by the ethical committee, involved translating T1w and T2w MR image series into CT images in a total of n=263 pairs of CT/MR series. Landmark-based registration was performed to align image pairs. We compared 2D paired (Pix2Pix, denoising diffusion implicit models (DDIM) image mode, DDIM noise mode) and unpaired (contrastive unpaired translation, SynDiff) image-to-image translation using "peak signal to noise ratio" (PSNR) as quality measure. A publicly available segmentation network segmented the synthesized CT datasets, and Dice scores were evaluated on in-house test sets and the "MRSpineSeg Challenge" volumes. The 2D findings were extended to 3D Pix2Pix and DDIM. Results: 2D paired methods and SynDiff exhibited similar translation performance and Dice scores on paired data. DDIM image mode achieved the highest image quality. SynDiff, Pix2Pix, and DDIM image mode demonstrated similar Dice scores (0.77). For craniocaudal axis rotations, at least two landmarks per vertebra were required for registration. The 3D translation outperformed the 2D approach, resulting in improved Dice scores (0.80) and anatomically accurate segmentations in a higher resolution than the original MR image. Conclusion: Two landmarks per vertebra registration enabled paired image-to-image translation from MR to CT and outperformed all unpaired approaches. The 3D techniques provided anatomically correct segmentations, avoiding underprediction of small structures like the spinous process.Comment: 35 pages, 7 figures, Code and a model weights available https://doi.org/10.5281/zenodo.8221159 and https://doi.org/10.5281/zenodo.819869

Multi-contrast MRI Super-resolution via Implicit Neural Representations

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework.This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr

Hypovitaminosis D in healthy pregnant women and their newborns in Greece

SUMMARYDespite vitamin D was discovered a hundred years ago, it has emerged as one of the most controversial nutrients and prohormones of the 21st century. Its role in calcium metabolism and bone health is indisputable, but its role in immune function and long-term health is also being discussed. A series of biological activities involving cell proliferation, differentiation and apoptosis correlate with vitamin D, actions that are equally important for fetal growth and development. Vitamino D deficiency has been increasing over the past 3 decades, with literature focusing on high-risk groups such as pregnant women and newbornsAIM OF THE STUDY: To evaluate the current vitamin D status in healthy pregnant women and their newborns living in Greece and assess possible associations between 25-hydroxyvitamin D [25(OH)D] and anthropometric features of their fetuses and newborns.MATERIALS & METHODS: 81 healthy women were monitored during pregnancy. Biochemical markers related to bone metabolism, such as 25(OH)D and PTH levels were measured in serum samples of mother-newborn pairs at 1st trimester of pregnancy and at delivery in mothers, in cord blood and at the 3rd day of life of newborns. RESULTS: Maternal 25(OH)D levels at 1st trimester of pregnancy (22.6±9.2ng/ml) were significantly higher than those at delivery (19.2±9.2ng/ml) (p30ng/ml]. Αντίστοιχα, το 55,8% των εμβρύων και το 38,4% των νεογνών είχαν επίπεδα 25(ΟΗ)D>30ng/ml. Σημαντικά θετική συσχέτιση βρέθηκε μεταξύ του μήκους του μηριαίου οστού στη διάρκεια της 22ης εβδομάδας της κύησης και των επιπέδων της 25(ΟΗ) D της μητέρας, στο πρώτο τρίμηνο της κύησης (r=0.36, p=0.048). Το μήκος σώματος του νεογνού (51.5±2.1cm) ήταν σημαντικά μεγαλύτερο στα νεογνά, των οποίων οι μητέρες είχαν επαρκή επίπεδα 25(ΟΗ)D στον τοκετό, συγκρινόμενο με το μήκος των νεογνών (50.6±2.0ng/ml), των οποίων οι μητέρες είχαν έλλειψη ή ανεπάρκεια 25(ΟΗ) D. Καμία συσχέτιση δεν διαπιστώθηκε, μεταξύ των επιπέδων της βιταμίνης D της εγκύου, και του βάρους γέννησης, ή της περιμέτρου κεφαλής, των νεογνών,στη γέννηση.ΣΥΜΠΕΡΑΣΜΑΤΑ: Από τη μελέτη μας προκύπτει ότι, ο επιπολασμός της υποβιταμίνωσης D στις εγκύους είναι υψηλός στην Ελλάδα, μια χώρα με άπλετη ηλιοφάνεια. Η υπoβιταμίνωση αυτή στις εγκύους συσχετίζεται με αντίστοιχη υποβιταμίνωση D των εμβρύων και των νεογνών τους. Επίσης, τα μειωμένα επίπεδα της 25(OH)D της μητέρας συσχετίζονται με μειωμένο μήκος του εμβρυϊκού μηριαίου οστού στην 22η εβδομάδα της κύησης, και ελαττωμένο μήκος σώματος του νεογνού, στη γέννησ

Μελέτη επιπέδων βιταμίνης D στην έγκυο και οι επιπτώσεις στο νεογνό

Παρά την ανακάλυψή της πριν από εκατό χρόνια, η βιταμίνη D έχει αναδειχθεί ως μία από τις πιο αμφιλεγόμενες θρεπτικές ουσίες και προορμόνες του 21ου αιώνα. Ο ρόλος της στο μεταβολισμό του ασβεστίου και στην υγεία των οστών είναι αδιαμφισβήτητος, αλλά συζητείται και ο ρόλος της στην ανοσολογική λειτουργία και τη μακροπρόθεσμη υγεία. Μια σειρά από βιολογικές δράσεις, που αφορούν τον πολλαπλασιασμό, τη διαφοροποίηση και την απόπτωση του κυττάρου, συσχετίζονται με την βιταμίνη D, δράσεις οι οποίες είναι εξίσου σημαντικές για την αύξηση και την ανάπτυξη του εμβρύου. Η έλλειψη βιταμίνης D, βαίνει αυξανόμενη τις 3 τελευταίες δεκαετίες, με το ενδιαφέρον της βιβλιογραφίας να επικεντρώνεται σε ομάδες υψηλού κινδύνου, όπως οι έγκυες και τα νεογνά. ΣΚΟΠΟΣ ΤΗΣ ΜΕΛΕΤΗΣ: Η αξιολόγηση των επιπέδων της βιταμίνης D σε υγιείς έγκυες γυναίκες και στα νεογνά τους που ζουν στην Ελλάδα και η αξιολόγηση πιθανών συσχετίσεων μεταξύ της 25-υδροξυ-βιταμίνης D [25 (OH) D] και των ανθρωπομετρικών χαρακτηριστικών των εμβρύων και των νεογνών τους. ΥΛΙΚΟ ΚΑΙ ΜΕΘΟΔΟΣ: Στη μελέτη συμμετείχαν 81 υγιείς έγκυες γυναίκες, οι οποίες παρακολουθήθηκαν κατά τη διάρκεια της κύησης, και τα υγιή τελειόμηνα νεογνά τους. Μελετήθηκαν τα δημογραφικά, κοινωνικά χαρακτηριστικά, και οι διατροφικές συνήθειες των εγκύων ,όπως επίσης και τα ανθρωπομετρικά χαρακτηριστικά των εμβρύων και νεογνών τους. Τα επίπεδα της 25(ΟΗ)D και της παραθορμόνης (ΡΤΗ), όπως επίσης και βιοχημικοί δείκτες που σχετίζονταν με το μεταβολισμό των οστών, μετρήθηκαν στον ορό των εγκύων, στο πρώτο τρίμηνο της κύησης, στον τοκετό, σε δείγμα αίματος από τον ομφάλιο λώρο , και στον ορό των νεογνών το τρίτο 24ωρο ζωής. ΑΠΟΤΕΛΕΣΜΑΤΑ: Τα επίπεδα της 25 (ΟΗ)D της μητέρας στη διάρκεια του πρώτου τριμήνου της κύησης ήταν σημαντικά υψηλότερα(22.6±9.2ng/ml) συγκριτικά με τα αντίστοιχα επίπεδα στον τοκετό (19.2±9.2ng/ml) (p<0.001). Επιπλέον τα επίπεδα της 25(ΟΗ)D ,από τον ομφάλιο λώρο, (21.3±9.3ng/ml), ήταν υψηλότερα από τα αντίστοιχα της μητέρας στον τοκετό (p=0.005), και από τα επίπεδα της 25(OH)D του νεογνού (19.4±10.4 ng/ml) (p=0.021), στο τρίτο εικοσιτετράωρο ζωής. Ποσοστό 57,3% των μητέρων στο πρώτο τρίμηνο της κύησης και 46,7% στον τοκετό είχαν επάρκεια βιταμίνης D [25(OH)D>30ng/ml]. Αντίστοιχα, το 55,8% των εμβρύων και το 38,4% των νεογνών είχαν επίπεδα 25(ΟΗ)D>30ng/ml. Σημαντικά θετική συσχέτιση βρέθηκε μεταξύ του μήκους του μηριαίου οστού στη διάρκεια της 22ης εβδομάδας της κύησης και των επιπέδων της 25(ΟΗ) D της μητέρας, στο πρώτο τρίμηνο της κύησης (r=0.36, p=0.048). Το μήκος σώματος του νεογνού (51.5±2.1cm) ήταν σημαντικά μεγαλύτερο στα νεογνά, των οποίων οι μητέρες είχαν επαρκή επίπεδα 25(ΟΗ)D στον τοκετό, συγκρινόμενο με το μήκος των νεογνών (50.6±2.0ng/ml), των οποίων οι μητέρες είχαν έλλειψη ή ανεπάρκεια 25(ΟΗ) D. Καμία συσχέτιση δεν διαπιστώθηκε, μεταξύ των επιπέδων της βιταμίνης D της εγκύου, και του βάρους γέννησης, ή της περιμέτρου κεφαλής, των νεογνών,στη γέννηση. ΣΥΜΠΕΡΑΣΜΑΤΑ: Από τη μελέτη μας προκύπτει ότι, ο επιπολασμός της υποβιταμίνωσης D στις εγκύους είναι υψηλός στην Ελλάδα, μια χώρα με άπλετη ηλιοφάνεια. Η υπoβιταμίνωση αυτή στις εγκύους συσχετίζεται με αντίστοιχη υποβιταμίνωση D των εμβρύων και των νεογνών τους. Επίσης, τα μειωμένα επίπεδα της 25(OH)D της μητέρας συσχετίζονται με μειωμένο μήκος του εμβρυϊκού μηριαίου οστού στην 22η εβδομάδα της κύησης, και ελαττωμένο μήκος σώματος του νεογνού, στη γέννηση.Despite vitamin D was discovered a hundred years ago, it has emerged as one of the most controversial nutrients and prohormones of the 21st century. Its role in calcium metabolism and bone health is indisputable, but its role in immune function and long-term health is also being discussed. A series of biological activities involving cell proliferation, differentiation and apoptosis correlate with vitamin D, actions that are equally important for fetal growth and development. Vitamino D deficiency has been increasing over the past 3 decades, with literature focusing on high-risk groups such as pregnant women and newborns AIM OF THE STUDY: To evaluate the current vitamin D status in healthy pregnant women and their newborns living in Greece and assess possible associations between 25-hydroxyvitamin D [25(OH)D] and anthropometric features of their fetuses and newborns. MATERIALS & METHODS: 81 healthy women were monitored during pregnancy. Biochemical markers related to bone metabolism, such as 25(OH)D and PTH levels were measured in serum samples of mother-newborn pairs at 1st trimester of pregnancy and at delivery in mothers, in cord blood and at the 3rd day of life of newborns. RESULTS: Maternal 25(OH)D levels at 1st trimester of pregnancy (22.6±9.2ng/ml) were significantly higher than those at delivery (19.2±9.2ng/ml) (p<0.001). Furthermore, umbilical 25(OH)D levels (21.3±9.3ng/ml) were higher than maternal at delivery (p=0.005) and neonatal levels (19.4±10.4 ng/ml) (p=0.021). Only 57,3% of the mothers at first trimester and 44.1% at delivery as well as 55.8% of the fetuses and 38.4% of the neonates had adequate vitamin D levels (25(OH)D <20ng/ml). A significant positive correlation was found between fetal femur length at 22nd week of gestation and maternal 25(ΟΗ)D at 1st trimester of pregnancy (r=0.36, p=0.048) while body length was significantly higher in newborns whose mothers had sufficient 25(OH)D levels (51.5±2.1ng/ml) compared with those whose mothers had insufficient or deficient 25(OH)D levels at delivery (50.6±2.0 ng/ml) (p=0.047). CONCLUSION: The study confirms inadequate levels of vitamin D in pregnant women in Greece associated with inadequate vitamin D levels of their fetuses and newborns. Also, the reduced maternal levels of 25 (OH) D are correlated with decreased fetal femur length, at 22nd weeks of gestation, and reduced neonatal body length

City Museum of Volos

This collection includes interviews conducted in the framework of the research project "Designing the Museum of the City of Volos". They cover various aspects of Volos' history that will be incorporated in future exhibitions of the Museum. The main topics covered in these interviews concern industrial work, multiculturalism, religious groups, the 1940s, immigration and daily life. Interview data (summaries, extracts, audio files) have been integrated into a keyword searchable database