Bookmarks¶
Maintainer: Dianne Patterson Ph.D. dkp @ email.arizona.edu
Date Created: 2018_09_09
Date Updated: 2019_10_31
Tags:
Also see the Glossary page.
Brain Atlases¶
- Brain Info is designed to help you identify structures in the brain.
- CORTICAL ATLAS PARCELLATIONS IN MNI SPACE
- NIF, the Neuroscience Information framework, is a dynamic inventory of web-based neuroscience resources.
- OBART The Online Brain Atlas Reconciliation Tool (OBART) aims to provide a quantitative solution to the so-called neuroanatomical nomenclature problem by comparing overlap relations between regions defined as spatial entities in different digital human brain atlases.
Computational Resources¶
- BIDS Brain Imaging Data Structure links
- Cyverse Cyberinfrastructure supporting online customizable virtual machines (Atmosphere), containerized apps (Discovery Environment) and data storage (Data Commons). You must request access to each service separately.
- Docker Containers
- GIT Repositories An excellent set of tutorials introducing the concept of code repositories and how to use them. Examples use Gitkraken which is a graphical git client available for free to academics.
- HPC Documentation University of Arizona High Performance Computing Documentation
- HPC Account Creation
- OOD Open On Demand Dashboard to interact with HPC resources.
- HPC Introduction
- Jupyter Org A free online unix terminal and Jupyter Notebook server.
- OpenNeuro A site that implements BIDS apps in an easily accessible gui interface. The catch is that you have to make your data public after a couple of years.
- REDCap A fully IRB-approved HIPAA-compliant web database application freely available to U of A researchers for capturing and querying data (e.g., we could have potential participants fill out their MRI screening here).
- Research Bazaar Unix Introduction
- SCIF The Scientific Filesystem
- Software Carpentry
- Software and Data Carpentry: University of Arizona
- Singularity Containers
fMRI Databases¶
- The Brede Database allows you to look up a brain region and discover what tasks activate it.
- Neurosynth is a platform that automatically synthesizes fMRI results across many studies.
- OpenNeuro See Computational Resources above. This is also a site to get publicly available BIDS compliant datasets.
Instructional: Neuroimaging Software and Concepts¶
- Andy’s Brain Book Andrew Jahn’s Read The Docs pages
- Andy’s Brain Blog Online tutorials and videos on a variety of topics: Afni, Eprime, Freesurfer, FSL, FSLeyes, Unix
- FMRIF Summer 2017 Course Materials fMRI powerpoints and video presentations
- GIFT Resources related to the GIFT ICA Matlab processing toolbox: presentations, a manual, sample data, a short video etc.
- Standard fMRI Analysis Tutorials Rajeed Raizada provides some excellent interactive Matlab tutorials for MVPA (multi-voxel pattern analysis) and SPM fMRI analysis.
- Resting State Analyis: How To Online resource from Jeanette Mumford et al.
MRI Concepts¶
- MRI Questions provides articles explaining how MRI works.
- MR-Tip is a glossary of MRI-related terms.
Neuroimaging Tools¶
- NITRC, the Neuroimaging Tools and Resource Collaboratory, is a huge database of neuroimaging tools and datasets.
Other¶
- The Massive Memory Database is a huge database of images useful for building visual stimulus sets. Images are organized into useful categories, like state pairs, exemplar pairs etc.
- Open Brain Consent A discussion of how to word your consent form to allow for sharing imaging data.