System Properties

Certain features of Jim are controlled by Java System Properties that can be set when launching Jim and its associated tools from the command-line or from a launch script. A System Property is set using a the option -D to the java command before the main class or the jar file in the java command line. For example:

java -DMyProperty=MyValue ...

sets a System Property called MyProperty to the value MyValue. The table below lists all System Properties that can affect Jim.

Property Name	Description	Possible Values
`analyze.compressed`	Whether Analyze 7.5 images should be stored compressed, or uncompressed.	`true \| false`
`analyze.createnonflipped`	Whether newly-created Analyze 7.5 images should have a non-flipped orientation. Overrridden by the setting in the User Preferences.	`true \| false`
`analyze.donotflipflipped`	Whether not to flip flipped Analyze 7.5 images. Overrridden by the setting in the User Preferences.	`true \| false`
`analyze.flipnonflipped`	Whether to flip non-flipped Analyze 7.5 images. Overrridden by the setting in the User Preferences.	`true \| false`
`analyze.fslorient`	Whether NIFTI images should be saved with an orientation that is compatible with FSL, where possible. Overrridden by the setting in the User Preferences.	`true \| false`
`analyze.spmorient`	Whether NIFTI images should be saved with an orientation that is compatible with SPM, where possible. Overrridden by the setting in the User Preferences.	`true \| false`
`analyze.warnnegheight`	Whether the user should be warned about negative pixel heights when loading Analyze/NIFTI images. Overrridden by the setting in the User Preferences.	`true \| false`
`analyze.warnnegwidth`	Whether the user should be warned about negative pixel widths when loading Analyze/NIFTI images. Overrridden by the setting in the User Preferences.	`true \| false`
`dongle.debug`	If `true`, licensing dongle access reports debugging messages to `System.out`.	`true \| false`
`license.debug`	If `true`, licensing reports debugging messages to `System.out`.	`true \| false`
`loadLibrary.debug`	If `true`, loading of external libraries reports debugging messages to `System.out`.	`true \| false`
`nifti.compressed`	Whether NIFTI images should be stored compressed.	`true \| false`
`nifti.fslcompatible`	Whether NIFTI images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI images should be prevented from being written without orientation information. Overrridden by the setting in the User Preferences.	`true \| false`
`nifti.onefile`	Whether NIFTI images should be stored in one file, or two.	`true \| false`
`Platform.GCP`	Determines whether Jim is run in "GCP" mode. In GCP mode, ROI files are saved with a checksum that ensures that manually editing causes corruption.	`true \| false`
`posixCompliant`	If `true`, the Image Converter will only create image files with POSIX-compliant names.	`true \| false`
`TextMode`	Determines whether Jim's tools are launched in text-only mode, or with a GUI.	`true \| false`
`umask`	Specifies the file-creation umask for all files newly-created by Jim.	Same format as the Unix umask.
`OutputType`	For certain command-line programs, determines the type of output image produced. These programs are: Converter MSIConverter RawConverter PictureConverter The System Property is overridden by the command-line option `-u,--output-type` for these programs.	`NIFTI-1 \| NIFTI-2 \| Analyze \| DICOM \| UNC`

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