Simulating Longitudinal Brain MRIs with Known Volume Changes and Realistic Variations in Image Intensity

Frontiers in Neuroscience
Bishesh KhanalXavier Pennec


This paper presents a simulator tool that can simulate large databases of visually realistic longitudinal MRIs with known volume changes. The simulator is based on a previously proposed biophysical model of brain deformation due to atrophy in AD. In this work, we propose a novel way of reproducing realistic intensity variation in longitudinal brain MRIs, which is inspired by an approach used for the generation of synthetic cardiac sequence images. This approach combines a deformation field obtained from the biophysical model with a deformation field obtained by a non-rigid registration of two images. The combined deformation field is then used to simulate a new image with specified atrophy from the first image, but with the intensity characteristics of the second image. This allows to generate the realistic variations present in real longitudinal time-series of images, such as the independence of noise between two acquisitions and the potential presence of variable acquisition artifacts. Various options available in the simulator software are briefly explained in this paper. In addition, the software is released as an open-source repository. The availability of the software allows researchers to produce tailored databases of im...Continue Reading


Jul 1, 1994·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·A SimmonsS R Arridge
Dec 1, 1995·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·H Gudbjartsson, S Patz
Nov 22, 1997·IEEE Transactions on Medical Imaging·P A Freeborough, Nick C Fox
Jun 9, 1998·IEEE Transactions on Medical Imaging·J G SledA C Evans
Jun 22, 2000·NeuroImage·John Ashburner, K J Friston
Aug 23, 2001·Medical Image Analysis·Mark Jenkinson, S Smith
Dec 17, 2002·NeuroImage·Stephen M SmithNicola De Stefano
May 13, 2006·IEEE Transactions on Medical Imaging·Bilge Karaçali, Christos Davatzikos
Nov 8, 2006·Topics in Magnetic Resonance Imaging : TMRI·Jennifer L Whitwell, Clifford R Jack
Nov 23, 2006·IEEE Transactions on Medical Imaging·Oscar CamaraNick C Fox
Nov 26, 2009·Journal of Cognitive Neuroscience·Daniel S MarcusRandy L Buckner
Feb 9, 2010·Nature Reviews. Neurology·G B FrisoniPaul M Thompson
Mar 12, 2010·Medical Image Analysis·Swati SharmaJ P Armspach
Oct 4, 2011·NeuroImage·Rong ChenEdward H Herskovits
Oct 30, 2012·NeuroImage·Owen CarmichaelAlzheimer's Disease Neuroimaging Initiative
Feb 7, 2013·Frontiers in Neuroscience·John Ashburner, Gerard R Ridgway
Apr 18, 2013·PLoS Computational Biology·Juergen DukartAlzheimer's Disease Neuroimaging Initiative
May 21, 2013·NeuroImage·Marco LorenziAlzheimer's Disease Neuroimaging Initiative (ADNI)
Aug 13, 2013·NeuroImage·Joaquim RaduaRaymond Salvador
Aug 31, 2013·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Swati SharmaJean-Paul Armspach
Mar 7, 2014·Frontiers in Neuroinformatics·Matthew McCormickLuis Ibanez
Sep 30, 2014·Neurobiology of Aging·Ferran PradosAlzheimer's Disease Neuroimaging Initiative
Oct 17, 2014·Medical Image Computing and Computer-assisted Intervention : MICCAI·Marc ModatSébastien Ourselin
Apr 11, 2015·Frontiers in Neuroinformatics·Brian B AvantsNicholas J Tustison
Apr 29, 2015·Frontiers in Neuroinformatics·Krzysztof J GorgolewskiDaniel S Margulies
Apr 21, 2016·PloS One·Alexander Schmidt-RichbergAlzheimer’s Disease Neuroimaging Initiative

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Nodding Syndrome

Nodding Syndrome is a neurological and epileptiform disorder characterized by psychomotor, mental, and growth retardation. Discover the latest research on Nodding Syndrome here.

LRRK2 & Microtubules

Mutations in the LRRK2 gene are risk-factors for developing Parkinson’s disease (PD). LRRK2 mutations in PD have been shown to enhance its association with microtubules. Here is the latest research.