309 citations · 381 across the 11 of their papers we have counts for
11 papers
JUMP: A joint multimodal registration pipeline for neuroimaging with minimal preprocessing
Adria Casamitjana, Juan Eugenio Iglesias, Raul Tudela +2
We present a pipeline for unbiased and robust multimodal registration of neuroimaging modalities with minimal pre-processing. While typical multimodal studies need to use multiple…
The TopCoW Challenge -- Topology-Aware Circle of Willis Segmentation for CT and MR Angiography
Kaiyuan Yang, Fabio Musio, Yihui Ma +112
The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to influence the risk, severity, an…
USLR: an open-source tool for unbiased and smooth longitudinal registration of brain MR
Adrià Casamitjana, Roser Sala-Llonch, Karim Lekadir +1
We present USLR, a computational framework for longitudinal registration of brain MRI scans to estimate nonlinear image trajectories that are smooth across time, unbiased to any ti…
Synth-by-Reg (SbR): Contrastive learning for synthesis-based registration of paired images
Adrià Casamitjana, Matteo Mancini, Juan Eugenio Iglesias
Nonlinear inter-modality registration is often challenging due to the lack of objective functions that are good proxies for alignment. Here we propose a synthesis-by-registration m…
Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas
Adrià Casamitjana, Marco Lorenzi, Sebastiano Ferraris +6
Joint registration of a stack of 2D histological sections to recover 3D structure (``3D histology reconstruction'') finds application in areas such as atlas building and validation…
DeepReg: a deep learning toolkit for medical image registration
Yunguan Fu, Nina Montaña Brown, Shaheer U. Saeed +14
DeepReg (https://github.com/DeepRegNet/DeepReg) is a community-supported open-source toolkit for research and education in medical image registration using deep learning.
3D Reconstruction and Segmentation of Dissection Photographs for MRI-free Neuropathology
Henry Tregidgo, Adria Casamitjana, Caitlin Latimer +9
Neuroimaging to neuropathology correlation (NTNC) promises to enable the transfer of microscopic signatures of pathology to in vivo imaging with MRI, ultimately enhancing clinical…
Introduction to Medical Image Registration with DeepReg, Between Old and New
N. Montana Brown, Y. Fu, S. U. Saeed +10
This document outlines a tutorial to get started with medical image registration using the open-source package DeepReg. The basic concepts of medical image registration are discuss…
Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge
Hugo J. Kuijf, J. Matthijs Biesbroek, Jeroen de Bresser +41
Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are o…
3D Convolutional Neural Networks for Brain Tumor Segmentation: A Comparison of Multi-resolution Architectures
Adrià Casamitjana, Santi Puch, Asier Aduriz +1
This paper analyzes the use of 3D Convolutional Neural Networks for brain tumor segmentation in MR images. We address the problem using three different architectures that combine f…
Voxelwise nonlinear regression toolbox for neuroimage analysis: Application to aging and neurodegenerative disease modeling
Santi Puch, Asier Aduriz, Adrià Casamitjana +8
This paper describes a new neuroimaging analysis toolbox that allows for the modeling of nonlinear effects at the voxel level, overcoming limitations of methods based on linear mod…