Sums:About

From Van Essen Lab

Jump to: navigation, search

Contents

Special Notice - SumsDB No Longer Available

SumsDB suffered a catastrophic failure in 2016 and due to a number of issues, SumsDB will not brought back online.

  • If you wish to access any of these datasets, You may obtain the login password by emailing sums@brainvis.wustl.edu. This requires a manual response on our side, so please be patient while awaiting login info.
  • The info buttons provide some information about the files contained within each archive, but be forewarned that the formatting is not pretty! It may also be slow to load. The download buttons should work once you’re logged in. Sorry that this is such a kludge, but hopefully you and others will find that it’s better than nothing. And it’s the best we’ll be able to do for legacy datasets in SumsDB.
  • Our lab remains strongly committed to sharing of extensively analyzed neuroimaging datasets. However, we are investing our efforts in a more forward-looking direction via the BALSA database (https://balsa.wustl.edu). In a nutshell, BALSA is to SumsDB what Connectome Workbench is to Caret visualization software. It has many nice features, and we hope that you and other investigators will switch from Caret to ‘Workbench’ and share your published results on BALSA (see https://www.ncbi.nlm.nih.gov/pubmed/27074495 for an article on BALSA).


About SumsDB

Image:SumsAboutImage.jpg NITRC_logo_Listed_Small.jpg


SumsDB (the Surface Management System DataBase) provides access to a growing body of neuroimaging and related data. WebCaret software provides online data visualization for datasets in SumsDB.

Main Categories of Data Based on Data Type and Usage

Atlas Datasets

  • Surface and volume data
  • Structural and functional data
  • Data on cerebral cortex and cerebellar cortex
  • Human data – normal and neurological/psychiatric disorders
  • Nonhuman primate data: macaque, chimpanzee, gorilla
  • Rodent: mouse and rat data

Searchable Stereotaxic Foci and fMRI Maps

  • Published data, curated and customized for data mining
  • Over 25,000 sterotaxic foci from nearly 1,000 published studies

Publication Associated Datasets

  • Underlay key figures in specific online publications:
  • Individual subject data and population data mapped to atlases

Project-Related Datasets

  • From various ongoing projects that serve archival purposes and sharing with selected collaborators
  • Data from FreeSurfer, CIVET, and other brainmapping software besides Caret

Tutorials

  • Documents and associated datasets from tutorials for both SumsDB/WebCaret and Caret.

Data Access and Security

  • SumsDB provides multiple levels of data access and security
  • Free (public) access (e.g., for data associated with published studies)
  • Data access restricted to collaborators in different laboratories
  • Owner-only access for work in progress

Data Organization

  • Download data as individual files or as collections (‘spec files’) customized for offline analysis in Caret

WebCaret

  • WebCaret provides online ‘Caret-style’ visualization without software or data downloads:
  • WebCaret ‘scenes’ facilitate rapid visualization of complex combinations of data
  • Bi-directional links between online publications and WebCaret/SumsDB provide:
  • Links from figures in online journal article to corresponding scenes in WebCaret
  • Links from metadata in WebCaret directly to relevant online publications and figures

Searching and Data Mining

  • Searching and data mining options using SumsDB and WebCaret:
  • Search by data type, filename, associated metadata (text-based search)
  • Spatially based queries
    • Proximity to stereotaxic coordinates
    • Overlap with selected fMRI activations (metric files)
    • Overlap with identified cortical areas (paint files)
  • Searches can be applied to:
    • Currently loaded datasets
    • ‘Processed’ datasets
    • All public SumsDB data
    • Restricted access data
  • Search results can be:
    • Viewed in WebCaret
    • Combined with other loaded data sets
    • Downloaded directly


Citing SumsDB

Use of SumsDB and datasets contained within SumsDB can be referenced to:

  • Van Essen, D.C., Harwell, J., Hanlon, D, and Dickson, J. (2005) Surface-Based Atlases and a Database of Cortical Structure and Function. In: Databasing the Brain: From Data to Knowledge (Neuroinformatics). S.H. Koslow and S. Subramaniam, eds., John Wiley & Sons, NJ, pp. 369-387
  • Dickson, J., Drury, H., and Van Essen, D.C. (2001) The surface management system (SuMS) database: A surface-based database to aid cortical surface reconstruction, visualization and analysis. Phil. Trans. Royal Soc, Ser B 356:1277-1292
Personal tools
Sums Database