A List of the Stand-Alone Tools

• A version with a graphical user interface (GUI). Most of these programs have names that end in ..Tool. In an MS Windows installation, the tools are available from the Start menu. See the linked manual pages for instructions on how to use them.
• A version that is for text processing only. For instructions on how to use them, run the tool program with the argument "--help" (e.g., "Algebra --help"). This will print out the usage message for the program. For more details about the meaning of the program arguments and options, see the equivalent GUI version of the program.

For example, image algebra can be performed in any of three ways:

• By calling up the Algebra tool from within Jim.
• By using the GUI version of Algebra as a stand-alone programme (AlgebraTool).
• By using the text-only version of Algebra as a stand-alone programme (Algebra).

On Unix systems (including Mac OS), scripts are provided to run the tools in either GUI or text-only (batch) mode. On MS Windows systems, batch (.bat) files are provided to run the tools in text-only mode. The scripts and batch files can be easily customised by you.

To see the program usage for any of the text-only tools, run the tool with the argument --help. This will show a usage message.

Here is a list of stand-alone tools, in alphabetical order.

• AIFResamplerTool and AIFResampler.
• AlgebraTool and Algebra.
• AnonymiseTool and Anonymise.
• BrainAtrophyTool and BrainAtrophy.
• BrainFinderTool, BrainFinder and BrainFinder2.
• BrainFUTool and BrainFU.
• CardiacTool and Cardiac.
• ConcatenatorTool and Concatenator.
• ConverterTool and Converter.
• CordFinderTool and CordFinder.
• CordFUTool and CordFU.
• DBManager.
• DCEMRITool and DCEMRI.
• DeMosaicTool and DeMosaic.
• DiffusionTool, WarpCorrection, DiffusionFitter and Tractography
• DimChangerTool and DimChanger.
• DynamicTool and Dynamic.
• FitterTool and Fitter.
• FuzzyConnectorTool and FuzzyConnector.
• InterleaverTool and Interleaver.
• Jim3D
• JMovie
• MaskerTool and Masker.
• ParticleTool and Particle.
• PerfusionTool and Perfusion.
• PictureConverterTool and PictureConverter.
• QFatTool and QFat.
• QueryRetrieve
• RawConverterTool and RawConverter.
• RegionTrainTool and RegionTrain.
• RegisterTool and Register.
• ResampleTool and Resample.
• ROIPropagateTool and ROIPropagate.
• SliceExtractorTool and SliceExtractor.
• StorageServerTool and StorageServer. The stand-alone program StorageServer acts to receive DICOM images as a background task. As such, the likely mode of operation is to start the StorageServer whenever your system boots. We include a sample script and instructions to start your StorageServer on bootup for Unix systems.
• ToRGBTool and ToRGB.
• TSRegisterTool and TSRegister.
• UnicorrTool and Unicorr.

The following are text-based programs that have no graphical user interface (GUI) equivalent. Click on the link to see the program usage.

• DicomSend
• DiffeoRegister (GUI interface to differomorphic registration is provided in the RegisterTool)
• Header
• JimStats
• Roi2Atlas
• Roivol
• RoiTotals
• LicensePing
• LicenseServer. The stand-alone program LicenseServer receives requests for licenses to run Jim from license clients, and manages the floating license pool. As such, the likely mode of operation is to start the LicenseServer whenever your system boots. You will also need to follow these instructions on Linux systems, these instructions on Apple Macs, and these instructions on Microsoft Windows so that your LicenseServer is to automatically started on bootup.
• ToAnalyze
• ToDICOM
• ToNIFTI1
• ToNIFTI2
• ToUnc