Main Features of Jim Version 6.0

Version 6.0 of Jim has many new features, including:

• New spinal cord segmentation tool (Cord Finder).
• New image de-mosaic tool for Siemens mosaic fMRI data.
• New image filtering options (Gaussian Blur, Sobel, Laplacian, Sharpen, Median, Morphological Operations) in Image Resampler.
• New text-mode JimStats program - produces output similar to fslstats.
• New 'Dyanamic Analysis' tool for general time-series analysis such as fMRI and ASL processing. Can use user-written plug-in analysis procedures.
• Improvements to Perfusion/DCE-MRI/Diffusion toolkits. These now allow different types of image masking: using Brain Finder to create a mask, using an image mask, using ROI masks, and using an intensity threshold.
• Improved motion correction in Perfusion/DCE-MRI. Greater flexibility of image smoothing options, allows selection the FWHM of the smoothing filter. The set of registered images produced is in the same format as the input image(s). For example, if a single input image containing alll time points is used, a single output image will be produced containing all registered time points.
• More than one overlay image can be overlaid at a time.
• Improvements to DCE-MRI tool: can use different types of reference image for R1 calculation, not just an M0 (fully-relaxed) image as before. Can use also an R1-map or a T1-map.
• DCE-MRI tool incorporates a new two-compartment exchange (2CX) model, and can also use plug-in user-defined models.
• In Image fitter, built-in preset functions do not need to be provided with initial guesses for the fit variables.
• Tools that produce parametric images by least-squares fitting (Fitter, Brain Perfusion, DCE-MRI and Dynamic Analysis) now have the option to write pixel values of NaN (Not-a-Number) into the output parameter images when the fitting fails, or (as was done pre- Version 6) a zero value. This is set in the user preferences.
• Image masking options now present with Image Algebra and Image Fitter tools.
• Linked cursors between main display and slave displays. Linked cursors also now available on Movie displays.
• ROIs can be visualised on images in slave displays without having to save and load ROIs into the slaves.
• 'Fast-save' file lists. Allows rapid saving to a user-defined set of file names, with logging of saves to file "FastSaveLog.txt" in current folder.
• Improved 3-D propagation of region-of-interest contours. When using 3-D propagation, contouring can be restricted to +/- number of slices. After 3-D propagation, there is an option to merge overlapping ROIs within a slice to prevent the creation of ROIs that contain other ROIs (holes).
• Different types of contouring - edge detection, intensity under mouse, mouse+/- delta, fixed intensity level.
• Increased control over contouring ROIs - can contour to centre or corner of pixels when pixel snap is turned on. Set in ROI preferences.
• Hollow ROIs. A hollow ROI can be created from two or more ROIs, where one ROI encloses the others entirely.
• Median intensity statistic shown in extended statistics for ROIs.
• ROIs can be saved to different ROI files based on Colour with "Save ROIs by Colour ...".
• Can lasso multiple ROIs with a mouse drag gesture in image slices where there are ROIs. In these slices, updating profiles and orthogonal views requires a mouse click (not updated on drags).
• When more than 1 ROI is selected, ROI statistics are shown for the combined ROIs.
• ROIs can be visualised on orthogonal views, in either outline or filled. Can be filled transparently.
• Erosion and dilation distances are now settable as a percentage of the pixel size in the ROI preferences dialog.
• Added ROI perimeter and surface area (surface area = perimeter × slice thickness) to totaliser.
• When saving ROIs, there is now an option set in the ROI Preferences to have the default save folder to either be the same folder as the current loaded image, or to have the folder unchanged when different images are loaded.
• ImageJ ROIs can be loaded into Jim.
• New keyboard short cut ('e') to activate the eraser tool for erasing/editing ROIs.
• Roaming response in the Image Fitter, Perfusion and DCE-MRI tools has been made more flexible and user-friendly. The response now responds to mouse clicks on the image, and Multiple ROIs/graph lines can be shown simultaneously on roaming response when more than 1 ROI is selected. Intensity for all ROIs may also be averaged to show the average response.
• Where different time points are in different image files, movies can be loaded from a stack of images, without going through the Image Concatenator.
• Jim has new command-line options to allow ROIs to be loaded into slave displays. JMovie has new command line options such that up to 5 linked Movie to be opened and images loaded.
• Both Jim and JMovie now have command-line options to allow Image Info to be opened from command line, and positioned/sized on screen.
• Orthogonal views in JMovie.
• JMovie has been reworked to make the settings for displaying multi-slice movies more logical.
• Regions of interest can be displayed on movies.
• Particle analysis has been revamped to make it quicker, and scale better with larger images when filling holes etc. Now includes the option to perform morphological operations on particles.
• Particle analysis - option to create ROIs that surround the particles that are found.
• Three modes of masking for Masker tool: generous, normal, conservative that determine whether a pixel is inside the mask, depending on the threshold percentage for how much of a pixel must be covered by an ROI (>0%, 50%, <100%).
• Image Algebra can be forced to output floating-point images.
• Large tool frames contain scrollable contents in case the Frame doesn't fit on the screen (making Jim more suited to computers with smaller displays).
• When loading an image, the image File Chooser shows basic details about the image (number of columns, rows, slices and frames).
• The size of image File Chooser, when first popped up, now depends on the number of image files in the current folder.
• User can now import colour mappings from file using:
  • 3 columns of text with R G B values, or
  • binary file of r,g,b, values (as used in ImageJ).
• When an image is loaded into a linked spawned display, Jim automatically goes to the same slice and sets image layout and zoom/scroll to same as that of the main display.
• Contrast/paging/magnification panel is now shrinkable/expandable to save screen space. Whether the panel is shrunk or expanded on startup can be set from the command line, and can be set separately for the Master and Slave displays.
• Tools that do not have an explicit button now save their last-used setting and will have the same configuration when next used.
• The "recently-used images" menu is now available in with a popup-menu on any ImageSelection Panel.
• Cross-reference display that allows slice location for the main image series to be visualised on a reference image (see View menu) that shares the same frame of reference as the main image.
• Improved textual search dialog for searching in image information.
• Can launch a File Manager from within Jim (if supported on the computer platform).
• Image interpolation setting on startup can be set separately for Master and Slave displays.
• Image Stats dialog now has a check-box to allow the exclusion of background zero-intensity pixels from the Histogram and statistics.
• DICOM Query/Retrieve incorporates additional search keys "Study Date", "Accession Number", and "Modality".
• "Save As" in DICOM format now handles 32-bit images by rescaling them to 16-bit.
• Update of private DICOM dictionaries for GE, Siemens and Philips scanners.
• Improved handling of DICOM images with non-default character sets - images with a single specific character set can now be handled. There is also now a user preference that causes all converted images to have only POSIX-compliant file names.
• Improved conversion of Bruker ParaVision™ images - many more parameters are stored to image header.
• Improved conversion of Varian/Agilent FDF images - correct image orientation is now maintained.
• Image Converter running in TextMode can now list images (option -l,--list) that would be converted, but without doing a conversion.
• When performing Image Conversion and saving to disk, there are user-settable options for what to do if the converted image already exists on disk: overwrite, don't overwrite, or create a copy with a file name appended with "_copy_X".
• A stack of ImportableImages (such as DICOM files) can be read directly as a an image stack (without first having to go through the Image Converter).
• For Fuzzy Connector and MS Lesion Finder, fuzzy threshold, weight on prior probability and connectivity in 3-D are recorded in the ROI file generated.

• 3-D visualisation. Triangulated surfaces; orthogonal cut planes; ROI surface generation.
• Diffusion toolkit. Diffusion tensor calculation and fibre tracking.
• Enhancements to Brain Finder. Can create a VRML (Virtual Reality Modelling Language) file of the brain surface which is depth shaded, and can be loaded into the 3-D Display. Enhanced brain extraction to remove bright areas in peri-orbital fat and vessels.
• Dimensionality changer. Change multiple 2-D images to 3-D; multiple 3-D images to 4-D; single 4-D to multiple 3-D; single 3-D to multiple 2-D images.
• More reliable registration.
• Time series registration. Create a pop-up graph showing Affine transform parameters over time. New "edge-matching" cost function.
• Improved image overlay, allowing colour images to be overlaid. Overlay images can have a completely transparent background.
• Different cursor types on orthogonal views, including "invisible".
• Enhanced screen capture allows export to different formats (GIF/JPEG/BMP/PNG).
• Improved interaction with ROIs.
  • Interactive Contours ROI display; updated as mouse is dragged across image.
  • Improved editing of Irregular ROIs.
  • ROIs can be flipped horizontally and vertically.
  • Morphological operations on ROIs (erode and dilate).
  • ROIs can have different colours.
  • 3-D contouring improved to propagate to more than one contour in adjacent slices if necessary.
• Improved interaction with main display: zoom with mouse scroll wheel; scroll on mouse drag gesture.
• Drag and drop to load images and ROIs.
• NIFTI and Analyze compressed images can be loaded directly.
• "Auto link" features for zoom, scroll and contrast setting.
• Multiple movies can run in synch.
• Image Converter supports DICOM 4 images with multiple slices per file.
• Imported and edited images can be saved in DICOM format.
• Images can be sent to a DICOM server, with ROIs being encapsulated as a private DICOM element.
• CT LUT preset windows.
• DICOM images can be loaded directly into Jim's display - no need to Convert.
• DICOM anonymiser. Reads any DICOM file and writes an anonymised copy.
• New "interoperability" preferences to improve operation with images that have been created using FSL.
• New startup options for Jim: windows and slaves can be sized and positioned from a command-line option; ROI toolkit can be started automatically and ROIs loaded.
• All applications have consistent, documented Exit Codes to signal errors.

• Fuzzy Connector tool. Isolate image features based on their "fuzzy connectedness" in multi-parametric image space.
• Semi-automatic multiple sclerosis lesion segmentation. Vastly speeds up calculating lesion volumes in PD/T₂-weighted/FLAIR/T₁-weighted MR images.
• Improved ROI creation and editing facilities:
  • New text ROIs for image labelling.
  • ROI annotation can be shown on the image.
  • Improved Irregular ROI editing, with smarter erasing and joining of ROIs.
  • "Intelligent" handle spacing on Irregular ROIs - spacing is adjusted according to the zoom setting. No more cluttered, overlapping handles.
  • Better interaction when moving ROIs - ROIs are drawn, not just the bounding box.
  • Point-and-press for contour ROI creation - point to the edge of the feature and press the 'c' key.
  • Line profiles for Line and Curved Line ROIs. Show the image intensities along a straight or curved path.
• Handling of NIFTI-1 format images, and expansion of the data types handled by Jim. Jim handles all these data types:
  • 1-bit binary.
  • 8-bit signed and unsigned byte.
  • 16-bit signed and unsigned short.
  • 32-bit signed and unsigned integer.
  • 64-bit signed long.
  • 32-bit float and 64-bit double float.
  • 2×32-bit complex.
  • 2×64-bit double complex.
  • R,G,B
• Greatly improved image registration. Registration allows more degrees of freedom, suitable for inter-subject registration and registration to a template image. It is integrated with the Image Overlay so the registration results can be displayed immediately and interactively.
• Interactive multi-planar reconstruction (MPR) allows interactive re-orienting and resampling of 3-dimensional images.
• Expanded user preferences, including a user-selectable look-and-feel, so you can choose the style of user interface that is most familiar to you.
• Improved image resampler handles images with dimensionality greater than 4.
• Image Importer, Image Converter and DICOM Query/Retrieve retrieve tools have been merged to give a consistent user interface and more user friendly importing and conversion of images. Converter handles Bruker ParaVision™ and Varian images. DICOMDIR files can be used to access CD-ROM contents, rather than scanning through all DICOM files.
• Improved Raw Data Converter, giving a wider range of data types, with clipping or coercion options if necessary.
• "Save As" function in Jim allow images to be saved in different image formats and with different data types.
• Minor improvements to Perfusion and DCE-MRI tools. In DCE-MRI tool with ROI analysis, image data and fit pop up in a graph.
• Result reports can be generated in text or PDF formats.
• Minor improvements to Brain finder:
  • Odd/even slice intensity corrections can be made.
  • User can choose starting guesses for peak locations in BPF calculation.
  • Graph pops up showing the fit used in the BPF calculation.
  • PDF report generation.
• Image Algebra and Image Fitter- images involved in algebra/fitting can be of mixed pixel data types. With the Fitter, output images can be forced to be in floating-point format, so that output scaling is no longer necessary.

• Region-of-interest analysis. Sophisticated ROI creation and editing using familiar user interface features.
• Brain atrophy assessment tools - fully automated atrophy assessments.
• MRI cerebral perfusion toolkit.
• Dynamic contrast-enhanced MRI toolkit.
• Particle analysis - pick out images features based on their brightness values.
• Improved Masker Tool. Automatically mask images using either ROIs or another image as masks.
• Image overlay - simultaneously display features from two images.
• Image algebra - perform pixel-by-pixel mathematical operations on multiple images.
• Image fitting - non-linear least-squares fitting for T₁ mapping, T₂ mapping - in fact any function can be fitted to your data.
• Registration - alignment of longitudinal and cross-modality image data.
• Uniformity correction - fully-automated bias correction.
• Movie display. Export GIF images, including animated GIFs from movies - ready to paste straight into your favourite presentation package or report.
• Orthogonal views of 3-D images - show axial/coronal/sagittal sections through the data.
• Line profiles.

• User preferences. Configure Jim to run just how you want it right from startup.
• Undo facility for region-of-interest editing.
• Support for DICOM standardised display of grayscale image. Make sure that your images look the same regardless of monitor type or ambient lighting conditions.

• Sophisticated image conversion - handling virtually all medical image formats.
• DICOM storage server, and DICOM query-retrieve tool.
• Image Resampler - crop, resize pixels and reorient images. Extract slices, concatenate and interleave images.
• Raw data importer - import your own data easily into Jim.
• Automatic handling of Analyze™ images in both big-endian (Sun) and little-endian (PC) format - completely transparently.

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