Software

Project on Scientific Transparency (PoST)

The Simons Foundation has generously helped us to develop software for scientific data management at Stanford.  We call this a Project on Scientific Transparency (PoST). PoST is designed to facilitate data and code sharing in neuroscience.  The project combines several objectives.  The concepts that were developed here are now being developed and extended for use at other sites by a startup, Flywheel Exchange.

In the Videos section of this web-page, you can find two talks about how PoST supports reproducible research in general and specifically for kids with difficulty learning to read.

Here, as an example, we include a pair of videos showing a person dragging MR data directories onto a browser. The data are uploaded to a site that processes the data and enters them into a data base.

The results of the processing are made available to the user both through the database, as the video shows, and also by a separate web-page that shows the analysis for the individual subject with respect to a population of subjects. An example of the analysis page is here

The database backend of the software developed in this project is also being used by Russ Poldrack and his colleagues to support their work on open data sharing.

Software 

Members of the lab (and I) maintain various MR physics and engineering tools in several github accounts. These include

  • ISETBIO - A subset of ISET that is merged with the Wavefront Toolbox for calculating the front-end of biological visual systems.  Joint work with Dave Brainard, Haomiao Jiang, and Jon Winawer.  See the ISETBIO wiki.
  • S-CIELAB (1998) image quality metric, Work with X. Zhang.  Updated version is in ISET.
  • The Vistalab respository has many open projects for MR, including VISTASOFT.  This software includes methods for analyzing fMRI, diffusion weighted imaging, anatomical data, and ECoG data.  Many people have contributed to this repository.

Data