Stanford Center for Reproducible Neuroscience held a BIDS info/help session on the Stanford University campus on June 29, 2018. We are making the slides used for the presentation available for all to review and look through. This presentation was used to introduce the attendees to BIDS, go through the different modality templates covered by BIDS, […]

Introduction Welcome back to the next tutorial in the tutorial series “Getting Started with BIDS”. In this tutorial, we will be utilizing an off-the-shelf solution called HeuDiConv. This tutorial will illustrate a detailed step-by-step guide on how to use HeuDiConv. The guide will take one subject and iteratively add one session at a time until the […]

Introduction Welcome to part 1B of the tutorial series “Getting Started with BIDS”. This tutorial will illustrate how one can automate the conversation of DICOMs into a valid BIDS dataset. This tutorial will follow the same workflow detailed in part 1A of this tutorial series. We will be using DICOMs from the Nathan Kline Institute (NKI) […]

Introduction Welcome to part 1A of the tutorial series “Getting Started with BIDS”. The tutorial series will introduce you to converting brain data into the BIDS organizational standard, provide an example of how to convert a dataset into BIDS (manually and an automated solution), and examine different off-the-shelf automated solutions. This tutorial will show a […]

Six months ago we launched a new platform for sharing and analyzing neuroimaging data – OpenNeuro.org. Over 600 users have registered on the platform since it launched, helping us test all of the new exciting features (such as client-side BIDS dataset validation, resumable uploads, and running analysis apps). We are now ready to make OpenNeuro […]

This post is part of a series of blog posts highlighting image analysis apps available on the OpenNeuro.org platform. It was contributed by Greg Kiar. Welcome to part one of a two-part spotlight on an original BIDS App [1], Neurodata’s MRI to graphs (ndmg; pronounced nutmeg) pipeline for connectome estimation. The ndmg pipeline (made in Python, hosted […]

Text of the Request for Information call: https://grants.nih.gov/grants/guide/notice-files/NOT-LM-17-006.html Recent years have proven that two components are essential for artificial intelligence breakthroughs: large, rich datasets and advanced algorithms. Advances in machine vision (especially object recognition) are a great example of this. The substantial increase in the accuracy of those systems was only possible due to availability of […]

This is a first episode of a series of blog posts highlighting image analysis apps available on the OpenNeuro.org platform. This piece was contributed by Gabriel A. Devenyi and Mallar Chakravarty. New to the OpenNeuro platform is the automatic structural segmentation pipeline MAGeT-Brain. Coming along with the pipeline are 5 expertly-segmented atlas/label combinations, at 0.3 mm isotropic, […]

We are pleased to announce that the OpenNeuro platform is now available for users at http://www.openneuro.org.  This platform represents the culmination of more than two years of work by the members of our center working closely with Squishymedia and supported by the Laura and John Arnold Foundation.  Here we would like to provide an overview […]

A few weeks ago we made an open call for applications for the 2nd CRN Coding Sprint. We received an overwhelming number of excellent applications. So many of the submitted projects exceeded our expectations we decided to sponsor more participants than initially planned. Here is the final list of accepted projects: Automate creation of BIDS-MEG […]

Stanford Center for Reproducible Neuroscience is proud to announce an open call for applications to the 2nd Annual Coding Sprint. Following the success of last year’s sprint, this year we will be focusing on three topics: Adding support for producing compatible outputs (BIDS Derivatives) to existing BIDS Apps for preprocessing. Containerizing and adding support for […]

Last Friday (2017/01/13) the Center for Reproducible Neuroscience organized an event at Stanford University to present two new MRI software tools built by the CRN: MRIQC – for quality control – and FMRIPREP – for robust preprocessing. The two tools have been under heavy development for that past year and the purpose of the event […]