Tools

NIDAG members are currently developing a number of different tools to facilitate open access to neuroimaging data. This page provides an overview of ongoing projects, with links to further information.

Automated Coordinate Extraction (ACE)

Developer(s): Tal Yarkoni
Status: Alpha
Open source: Yes
Language(s): Ruby, but ports are welcome
Open to new contributors: Yes please!
Link: http://github.com/NIDAG/ACE

ACE is a suite of Ruby scripts designed to automatically extract stereotactic coordinate information from full-text HTML versions of neuroimaging articles. It takes HTML files as input, parses the HTML, and saves a bunch of information to a relational (MySQL) database. As part of the basic processing stream, ACE performs the following steps:
  • Extracts foci reported in tables anywhere within the article (ACE currently does *not* look for foci reported in the body of an article).
  • Extracts basic metadata for each article (authors, source, etc.).
  • Generates a list of all words that occur at least once in the body of the article, with an associated frequency count for each word.
Additionally, ACE provides limited functionality for searching through the extracted data and exporting results in a number of different formats.

At present, ACE is intended for use as a Ruby library rather than a standalone package. Some familiarity with the Ruby programming language will most likely be required; we don't (currently) provide a graphical interface. In the long term, we plan to transition the tools to a web-based interface.

For further information, see the github page or email Tal Yarkoni.

FSL Automated Coordinate Extraction (FACE)

Developer(s): Jan Derrfuss
Status: Alpha
Open source: Yes
Language(s): Perl
Open to new contributors: Yes
Link: FACE.zip (includes perl script and config file)

FACE is a Perl script that automatically extracts information from an FSL gfeat directory. The following information is retrieved:
  • Feat version
  • Number of subjects
  • Spatial smoothing
  • Template brain
  • Type of thresholding
  • Peak coordinates
  • Peak z scores
  • Number of voxels in a cluster
Before running the script, the path to the gfeat directory and the desired contrast of parameter estimates have to be specified in a config file. The script generates output files that conform to YAML standards. In the long term, these output files could be uploaded to a neuroimaging result database.

For further information, email Jan Derrfuss.

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FACE.zip
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NIDAG Member,
Jan 6, 2011, 11:41 AM
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