Bayesian analysis of retinotopic maps
Abstract
Human visual cortex is organized into multiple retinotopic maps. Characterizing the arrangement of these maps on the cortical surface is essential to many visual neuroscience studies. Typically, maps are obtained by voxel-wise analysis of fMRI data. This method, while useful, maps only a portion of the visual field and is limited by measurement noise and subjective assessment of boundaries. We developed a novel Bayesian mapping approach which combines observation-a subject's retinotopic measurements from small amounts of fMRI time-with a prior-a learned retinotopic atlas. This process automatically draws areal boundaries, corrects discontinuities in the measured maps, and predicts validation data more accurately than an atlas alone or independent datasets alone. This new method can be used to improve the accuracy of retinotopic mapping, to analyze large fMRI datasets automatically, and to quantify differences in map properties as a function of health, development and natural variation between individuals.
Data availability
All data generated or analyzed in this study have been made public on an Open Science Foundation website: https://osf.io/knb5g/Preprocessed MRI data as well as analyses and source code for reproducing figures and performing additional analyses can be found on the Open Science Foundation website https://osf.io/knb5g/.Performing Bayesian inference using your own retinotopic maps.To perform Bayesian inference on a FreeSurfer subject, one can use the neuropythy Python library (https://github.com/noahbenson/neuropythy). For convenience, this library has also been packaged into a Docker container that is freely available on Docker Hub (https://hub.docker.com/r/nben/neuropythy).The following command will provide an explanation of how to use the Docker:> docker run -it --rm nben/neuropythy:v0.5.0 register_retinotopy --helpDetailed instructions on how to use the tools documented in this paper are included in the Open Science Foundation website mentioned above.
-
Bayesian Models of Human Retinotopic OrganizationOpen Science Framework, osf.io/knb5g/.
Article and author information
Author details
Funding
National Eye Institute (R01 EY027401)
- Jonathan Winawer
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: This study was conducted with the approval of the New York University Institutional Review Board (IRB-FY2016-363) and in accordance with the Declaration of Helsinki. Informed consent was obtained for all subjects.
Copyright
© 2018, Benson & Winawer
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 5,178
- views
-
- 523
- downloads
-
- 109
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Immunology and Inflammation
- Neuroscience
Acute retinal ischemia and ischemia-reperfusion injury are the primary causes of retinal neural cell death and vision loss in retinal artery occlusion (RAO). The absence of an accurate mouse model for simulating the retinal ischemic process has hindered progress in developing neuroprotective agents for RAO. We developed a unilateral pterygopalatine ophthalmic artery occlusion (UPOAO) mouse model using silicone wire embolization combined with carotid artery ligation. The survival of retinal ganglion cells and visual function were evaluated to determine the duration of ischemia. Immunofluorescence staining, optical coherence tomography, and haematoxylin and eosin staining were utilized to assess changes in major neural cell classes and retinal structure degeneration at two reperfusion durations. Transcriptomics was employed to investigate alterations in the pathological process of UPOAO following ischemia and reperfusion, highlighting transcriptomic differences between UPOAO and other retinal ischemia-reperfusion models. The UPOAO model successfully replicated the acute interruption of retinal blood supply observed in RAO. 60 min of Ischemia led to significant loss of major retinal neural cells and visual function impairment. Notable thinning of the inner retinal layer, especially the ganglion cell layer, was evident post-UPOAO. Temporal transcriptome analysis revealed various pathophysiological processes related to immune cell migration, oxidative stress, and immune inflammation during the non-reperfusion and reperfusion periods. A pronounced increase in microglia within the retina and peripheral leukocytes accessing the retina was observed during reperfusion periods. Comparison of differentially expressed genes (DEGs) between the UPOAO and high intraocular pressure models revealed specific enrichments in lipid and steroid metabolism-related genes in the UPOAO model. The UPOAO model emerges as a novel tool for screening pathogenic genes and promoting further therapeutic research in RAO.
-
- Computational and Systems Biology
- Neuroscience
Diffusional kurtosis imaging (DKI) is a methodology for measuring the extent of non-Gaussian diffusion in biological tissue, which has shown great promise in clinical diagnosis, treatment planning, and monitoring of many neurological diseases and disorders. However, robust, fast, and accurate estimation of kurtosis from clinically feasible data acquisitions remains a challenge. In this study, we first outline a new accurate approach of estimating mean kurtosis via the sub-diffusion mathematical framework. Crucially, this extension of the conventional DKI overcomes the limitation on the maximum b-value of the latter. Kurtosis and diffusivity can now be simply computed as functions of the sub-diffusion model parameters. Second, we propose a new fast and robust fitting procedure to estimate the sub-diffusion model parameters using two diffusion times without increasing acquisition time as for the conventional DKI. Third, our sub-diffusion-based kurtosis mapping method is evaluated using both simulations and the Connectome 1.0 human brain data. Exquisite tissue contrast is achieved even when the diffusion encoded data is collected in only minutes. In summary, our findings suggest robust, fast, and accurate estimation of mean kurtosis can be realised within a clinically feasible diffusion-weighted magnetic resonance imaging data acquisition time.