BrainMap GingerALE 3.0.2 ReadMe

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What's New in Version 3.0.2 [May 16, 2019]

Recent Changes:

What's New in Version 3.0.1 [May 2, 2019]

Recent Changes:

What's New in Version 3.0 [February 5, 2019]

Major Changes:

Cluster Statistics:


Minor Changes:

What's New in Version 2.3.6 [April 26, 2016]

Algorithm Bug Fix:

Other Bug Fix:


What's New in Version 2.3.5 [November 19, 2015]

What's New in Version 2.3.4 [October 12, 2015]

Includes Java!

The Mac and PC versions now include their own copy of Java 8. This increases the size of the download by about 50MB, but gets rid of all issues related to incompatable Java versions. Those using the jar version will still need a copy of Java.

Bug fixes:

What's New in Version 2.3.3 [May 11, 2015]

Bug fixes:

Correction to False Discovery Rate calculations (Thanks, Chris)

Command-line interface recognizes threshold settings and saves thresholded results (reintroduced issue from 2.3.2)

What's New in Version 2.3.2 [May 7, 2014]

Various small improvements:

Renamed the included mask images to Tal_wb and MNI_wb (see command-line options) (Thanks cmcnorgan!)

Fixed getALE2Contrast command-line bug related to Cluster-Level thresholds (Thanks cmcnorgan!)

Fixed getALE2 command-line bug which interfered with threshold settings (Thanks cmcnorgan!)

Fixed conjunction xls file name bug (Thanks Matthew!)

What's New in Version 2.3.1 [September 30, 2014]

Updated Users' Manual

Various small improvements:

What's New in Version 2.3 [January 11, 2013]

More Thorough Data Set Checking:

Single-study analyses will show warnings for:

Contrast analyses will show warnings for:

Improved Data History:

Various small improvements:

What's New in Version 2.2 [May 14, 2012]

New Thresholding Methods

New Contrast Features

Improved Data History:

Various small improvements:

What's New in Version 2.1.1 [October 11, 2011]

Various small improvements:

What's New in Version 2.1 [August 30, 2011]

Contrast Two Data Sets:

When comparing two data sets A & B, GingerALE will save output files for A-B, B-A and A_conj_B for contrasts and conjunction. Also updated command-line tools for contrasts.

Simplified Data History:

Removed statistics on thresholds that weren't used to make data history more clear.

Foci Rounding Bug:

Fixed rounding bug in Convert Foci when negative coordinate values ended in ".99". (Thanks, Russ Poldrack)

What's New in Version 2.0.4 [August 10, 2010]

Preferences Window bug:

Fixes a bug from GingerALE 2.0.3 which prevents the preference window from showing. (Thanks, Karvonen)

Default Browser:

Improved checking of your default browser (Thanks, Bare Bones Browser Launch)

What's New in Version 2.0.3 [August 7, 2010]

ALE FWHM bug fix:

GingerALE 2.0.1 and 2.0.2 incorrectly use the first experiment's number of subjects and FWHM for all subsequent experiments. 2.0.3 uses the appropriate FWHM values. (Thanks, Danilo!)

P value optimization:

When computing P values, GingerALE uses less memory especially for smaller data sets.

What's New in Version 2.0.2 [July 28, 2010]

New "Non-Additive" ALE Method bug fix:

GingerALE reported using the wrong ALE method in the Data History. It has now been fixed. (Thanks, briandh)

What's New in Version 2.0.1 [July 6, 2010]

New "Non-Additive" ALE Method:

In GingerALE's preferences you can choose to use a modified algorithm for computing the ALE statistic. The standard modelled activation maps are computed as the cumulative union of gaussians at each foci within the experiment. The new method uses the maximum value from nearby gaussians, which limits the effect of multiple nearby foci within an experiment. This changes the focus from concordance between foci to concordance between experiments.

FWHM & more:

What's New in Version 2.0 [August 24, 2009]

New Algorithm:

MNI Support:

Other New Features:

Bug Fixes:

What's New in Version 1.1 [October 3, 2007]


A new anatomical template is included to be used for viewing ALE results. This template corrects a small defect in the previous template and offers a better representation of Talairach space. We also updated the masks in GingerALE to match this revised template.

GingerALE automatically changes the mask to match ALE images. Thus, if you open existing ALE files that were created prior to this release, GingerALE will utilize the mask that was previously implemented. Nevertheless, to ensure that your images are as accurate as possible, we suggest that re-run your meta-analysis using the new mask/template.




What's New in Version 1.0 [April 13, 2007]

New Tools:






Java: The Mac and Windows versions include their own copy of Java 8, so Java version conflicts and updating are no longer an issue. The compromise is that it is now about 150 MB larger. The jar version is available without embedded Java as well.

Windows: Download the zip and unzip it to get a "GingerALE 3.0.2" folder which contains:

Macintosh: Download the app. It's using a Disk Image (.dmg), which is like a virtual file, but it includes a secure signature that lets your Mac show fewer scary "Unknown Developer" warnings. If your browser doesn't automatically open the xip file, just double-click it and you should get Drag to your Applications folder, or wherever you prefer, and start it up.

Other Systems: Get Java Version 8 or newer at Oracle's official site: Download GingerALE.jar. You may be able to run GingerALE by double clicking on the jar. Alternatively, use the command: java -cp your/path/to/GingerALE.jar org.brainmap.GingerALE GingerALE has several other command-line options.


Feedback & Help: The GingerALE Forum is available for reporting bugs, or questions about GingerALE or performing meta-analyses.

The BrainMap Development Team

Copyright © 2003 Research Imaging Institute. All rights reserved.