# Bayesian Analysis of Retinotopic Maps
Noah C. Benson<sup>1,*</sup> and Jonathan Winawer<sup>1,2</sup>
<sup>1</sup> Department of Psychology, New York University
<sup>2</sup> Center for Neural Sciences, New York University
<sup>*</sup> To whom correspondences should be addressed; [email@example.com](mailto:firstname.lastname@example.org).
Benson NC, Winawer J (2018) Bayesian analysis of retinotopic maps. *eLife*. **7**: e40224. DOI:[10.7554/eLife.40224](https://doi.org/10.7554/eLife.40224)
This wiki documents the data and code repository for the paper "Bayesian Analysis of Retinotopic Maps" by Noah C. Benson and Jonathan Winawer. This OSF repository contains all preprocessed data and code used in writing the paper as well as instructions for using the tools documented in the paper.
It is the hope of the authors that this wiki and the tools documented here will be of considerable use to the scientific community. To this end, we ask that you please contact us if you are unable to use these tools or have questions about them.
## Using these Tools
If you want to use the tools described in our paper, see the [usage page](../Usage).
## Example Subject
For a simple tutorial on running the Bayesian inference on an example subject from our dataset, see the [example page](../Example).
## Reanalyzing/Browsing the Data
The various files in this repository contain all the data needed to recreate the figures and analyses included in the paper. The [data page](../Data) of this wiki explains what data is included and what format it is in.
## OSF Repository Manifest
This repository contains files that can be broadly categorized as either [code](../Code) or [data](../Data). Note that all files can be downloaded using the `download.sh` script provided as part of this archive.
Code files explicitly document the methods reported in the paper and the algorithms we used to analyze our data. The following code files are documented on the [Code page](../Code):
* The visualization notebook, `v123-visualization.nb`
* The [Neuropythy](https://github.com/noahbenson/neuropythy) repository archive; note that the version of this library used to prepare the paper (v0.5.0) has also been permanently archived with the following DOI:[10.5281/zenodo.1312983](https://doi.org/10.5281/zenodo.1312983)
* The Neuropythy docker image, `neuropythy-docker-image.tar.gz`, which provides the Neuropythy library packaged in a virtual execution environment; note that this version of the docker-image has also been tagged on its [Docker hub page](https://hub.docker.com/r/nben/neuropythy) as [nben/neuropythy:v0.5.0](https://hub.docker.com/r/nben/neuropythy/tags/)
* The `download.sh` script
Data files contain both preprocessed experimental data and analysis data as well as cache data generated while writing the paper. These files are documented on the [Data page](../Data):
* The FreeSurfer subject directories, `freesurfer_subjects.tar.gz`
* The measured retinotopic maps, `retinotopy.tar.gz`
* The inferred retinotopic maps, `analyses.tar.gz`
* The figures, `figures.tar.gz`
* Various cached analysis data, `cache.tar.gz`
* The [Wang et al., (2015)](https://doi.org/10.1093/cercor/bhu277) atlas, `wang2015.tar.gz`