BrainMap GingerALE 1.1 ReadMe
Installation
Requirements:
- Java 1.4 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 1.1".
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 1.1". 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 -classpath /path/to/GingerALE.jar org.brainmap.GingerALE
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
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