BrainMap GingerALE 2.0.4 ReadMe
Installation & Support
What's New in Version 2.0.4
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
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
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
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:
- FWHM values now match Eickhoff 2009 calculations, see graph
- Foci without subject information default to using a FWHM of 19.07
- Data History reports range of FWHM used and the total number of subjects (Thanks, Dan Shaw)
- ALE statistic calculation now includes 2x2x2 voxel size (Thanks, Peter Turkeltaub)
- Added option in preferences for an additional FWHM "fudge factor"
What's New in Version 2.0
New Algorithm:
- Requires subject data within foci text (Supported by Sleuth 1.2)
- Temporarily saves activation maps to disk (<1MB per experiment)
- Subtraction foci are not supported in this release
- ALE and P Value images can not be loaded from file in this release
MNI Support:
- Supports MNI reference space throughout, chosen in the preferences
- Shows chosen coordinate system in Foci section
- Automatically changes reference space to match the reference space of the foci data (if using Sleuth 1.2)
- Supports MNI in coordinates by transforming them, then using talairach labels
Other New Features:
- Improved Data History with more information (mask details, experiment tables, minimum recommended cluster volume) and added the ability to save it at any time (File → Save Data History)
- Simplified the interface into 3 steps: ALE, Thresholding & Cluster Analysis
- Improved command-line support with standardized arguments & error messages, and several more options (output file, mask size, reference space)
Bug Fixes:
- Changed clustering algorithm to better match FSL & Mango (Thanks Matt C.)
- Fixed NIfTI extension data to add FSL support (Thanks Matt W.)
- Fixed a cluster analysis bug to handle 0 clusters (Thanks Synge)
- Fixed a Foci Image bug that caused the image not to be saved
- Fixed data history bugs: mask dimensions and % of voxels greater than pN now reported correctly
- Supports Spaces in Mac OS X
What's New in Version 1.1
Masks:
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.
Foci:
- A warning is displayed if any lines in the text file of input foci were not correctly interpreted due to improper formatting
Clusters:
- “Show all local extrema” was added to Preferences that will search the ALE clusters and report not only the maximum values of the ALE statistic, but also the submaxima values that extend along the whole volume of the cluster
- Added a preference to limit the local extrema to the just maximum and minimum values of the cluster
- Fixed a bug that stopped the Clusters step from being re-run
- Fixed a bug that caused Cluster Statistics to hang when finding labels from the Talairach Daemon
Other:
- Added "Check For Updates" in the Help menu
- File dialogs for "Open ALE Scores" and "Open P Values" now gray-out images which aren't ALE or P Value images from the list of possible input files
- Temp files created during permutations are now more reliably deleted
- Export Foci Image saves to the path chosen instead of the default output path
What's New in Version 1.0
New Tools:
- Added "Convert Foci" option to convert your coordinates from MNI space to Talairach space using multiple versions of the icbm2tal (Lancaster) and mni2tal (Brett) tranformations
- Added "Export Foci Image" to create a NIfTI file of your foci points. No blurring of the coordinates is performed when this image is created
Foci:
- Now included as a separate section of the interface before ALE in order to see how many coordinates and experiments are included in your meta-analysis
- Output file names are updated when foci are loaded
- Foci name is included in the window title
Preferences:
- Added option for less conservative (larger) mask of Talairach space to analyze foci on the border of the brain
- Added option to choose pN or pID as threshold value during FDR procedure
- Re-grouped the preferences and improved the interface
Other:
- GingerALE is now a stand-alone application, separate from Sleuth (previously known as Search&View)
- Many small interface changes and larger code structure changes
- Now distinguishes between ALE & P Value images when loading files
- Added "Show Manual...", "Show Read Me..." and "Show License..." to the Help menu. These options show the manual (in .pdf format), readme, and license files in your default web browser
Installation
Requirements:
- Java 1.5 or better
- 256 MB RAM
Macintosh:
If the disk image doesn't open automatically, then double-click on
GingerALE.dmg. This should create a disk image called "GingerALE 2.0.3".
Open the disk image and drag GingerALE to the Application folder.
Double-click GingerALE to run the program.
Windows:
If the file doesn't unzip automatically, then double-click on
GingerALE.zip. This should expand the file so that you should now have
a folder called "GingerALE 2.0.3". Open the folder and follow the
instructions in "How to Install GingerALE.txt". Double-click on
GingerALE.exe to run the program.
Other Operating Systems:
Put GingerALE.jar where ever you like. You may be able to run GingerALE
by double clicking on the jar. Alternatively, use the command:
java -cp /path/to/GingerALE.jar org.brainmap.GingerALE
Support
Feedback & Help:
There is a new forum for feedback and support.
Please report any bugs you find while using this software.
Or, send us your comments and questions about using GingerALE or performing meta-analyses.
Thanks,
The BrainMap Development Team