Main New Features of Jim Version 9

Version 9 of Jim has many new features, including:

• Improved brain atrophy/lesion volume measurement with more automated segmentation.
• Quantification of spinal cord atrophy longitudinally.
• Maximum intensity projection (MIP).
• Image synthesizer: generate synthetic images where you have PD, T₁ and T₂ maps.
• Semi-automated endo- and epi-cardial border propagation in Cardiac Analysis tool.
• Extended Cardiac Analysis. Short axis LV Function (stroke volume and ejection fraction) and Strain analysis (from tagged or non-tagged cine images) added to Cardiac Analysis tool.
• Chemical exchange saturation transfer (CEST) processing module.
• Support for NIFTI-2 format.
• Improved Brain Finder (Mark 2), allowing the user to specify their own template image and brain mask for registration.
• Logical operations on ROIs (AND NOT, UNION, INTERSECT, XOR).
• Improved 3-D display with better transparency. Ability to read and write 3-D Wavefront OBJ and STL files, as well as VRML files.
• Export movies from JMovie to AVI and QuickTime formats, as well as animated GIFs.
• Improved reliability of ROI propagation tool.
• New "Patch Similarity" noise suppression filter in Image Resampler.
• Intensity values are remapped according to slope and intercept values in header (NIFTI and UNC images). DICOM images are automatically remapped and converted to floating-point pixel intensity values on conversion if rescale slope≠1 and rescale intercept≠0.
• Improved appearance on HiDPI screens.
• Image Converter can save as one-file-per-slice DICOM format.
• ROI Totaliser now shows volumes and intensity statistics for each individual VOI.
• New stand-alone program RoiTotals that calculates ROI and "roi_group.html">VOI statistics and outputs them in the same format as the ROI Totaliser.
• On operating systems that support the POSIX standards, file permissions on file/folder creation are set from the system property "umask".
• New command-line option for Jim to launch the Image Overlay dialog and load up to 3 images as overlay images, together with their colour mappings. Run Jim from the command-line with option -h to see all options.
• Set "default" colour mappings for the overlay images (up to 3 overlays), so that the selected colour mapping is used when a new image is loaded into an overlay.

• New, sophisticated brain atrophy assessment tool with optional semi-automatic white-matter lesion segmentation. For whole-brain, grey-matter and white-matter atrophy.
• New non-linear (diffeomorphic) image registration, in addition to affine registration.
• New quantitative fat/water separation from gradient-echo images with different echo times.
• New arterial spin-labelling (ASL) analysis module for the Dynamic Analysis tool.
• New converter for picture formats. Can convert JPEG, GIF, BMP, PNG, TIFF, PNM, PBM, PGM and PPM pictures to NIFTI, Analyze, DICOM or UNC format. Pictures can be stacked in 3-D to create a 3-D volume.
• Improved non-uniformity (bias field) correction. This also improves the results from the Brain Finder and Brain Follow Up tools.
• Improved Brain Finder. New, more reliable alternative algorithm that uses a template for the initial brain segmentation and needs no selection of the threshold fraction. Existing algorithm has been parallelized and is faster on multi-core processors.
• Improved Multi-Planar Reconstruction, with more intuitive interactions. Resampling volume geometry can be saved to disk and retrieved from disk so that the same MPR can be applied to multiple images.
• Improved affine registration. Can now produce 'half-way' registered images. Allows the inverse of any transform (rtp file), to be applied. Images can be aligned using position and orientation information present in the image headers.
• Improved Least-Squares fitter, with much faster fitting for "standard" fitting functions. Also, for FLASH T₁ fitting, a flip angle calibration image can be input.
• Improved anonymisation. As well as DICOM, NIFTI, UNC and Analyze images can now be anonymised. A record is made of the anonymisation date/time and which DICOM Elements were anonymised.
• Extended Image Resampler now allows images to be flipped horizontally, vertically or the slice order to be reversed.
• Extended Image Masker tool allows the creation of binary masked images.
• Jim's 3D display can create movies (QuickTime or AVI) of activities shown in the 3-D display.
• For diffusion-weighted image warp correction, this is now integrated with motion correction.
• In the ROI Toolkit, ROIs can be 'grouped' together. Annotation and colour can be set for a group of ROIs. Automatic grouping of ROIs based on their 3-D connectivity.
• In the ROI Toolkit, image pixels can be manually 'painted' (e.g. for lesion filling). The paint intensity value can be typed in, or picked from the image with an intensity picker.
• More minor improvements:
  • In ROI Toolkit, ROIs can be pasted to a certain range of slices.
  • Graph data and tables can be written in space-separated, tab-separated or comma-separated format; the desired format is set in the User Preferences. Arterial input function data can be read in space-separated, tab-separated or comma-separated format.
  • Image Converter has a new option (-b) to create b-value, gradient vector and b-matrix text files on conversion of diffusion-weighted images. Coordinate system for gradients is the image row/column/slice directions.
  • From the Image Converter, images can be directly dragged-n-dropped onto multiple input image selection panels (e.g. onto Image Interleaver input).
  • The ToNIFTI, ToAnalyze, ToDICOM and ToUnc text-only programs now allow the batch conversion of all images within a folder and sub-folders. There is a new option to force all images in the batch to have the same "Study Time" and "Study Instance UID" so that converted images can be forced to be part of the same study.
  • The font size for Text components in the user interface can be set in the user's preferences to aid readability on high-resolution computer monitors.
  • The Image Overlay dialog can be launched from the command-line, with loading of an overlay image.
  • Spatial filters in the Image Resampler now handle floating-point images with NaN (not-a-number) values by substituting values which are the mean of adjacent non-NaN pixel values.
  • Jim works with IPv6 Internet addresses.

These features are on top of those of Version 7:

• Smoother handling of DICOM images - no need to convert to another format under most circumstances.
• DICOM Storage server now supports Query/Retrieve, with database backing.
• Image database manager, with support for clinical trials.
• New tool for mapping lesion changes for longitudinal studies.
• New tool for ROI propagation.
• New tool for cardiac segmental analysis.
• New tool to combine three greyscale images into a single colour image (ToRGB).
• Image Converter is able to handle computed Bruker images from Xtip.
• Drag 'n' drop from Image Converter and DICOM query-retrieve into display and into all Image Selection Panels.
• Labels for patient name, patient ID and study description are configurable in width in the Image Converter.
• Image preview in Image File Chooser.
• Re-mappable keyboard accelerators. New keyboard accelerators added for ROI creation.
• New ROIs types with smooth outlines - Spline and OpenSpline.
• Improved user interaction when contouring at fixed level, mouse+Δ and mouse-Δ. Press down mouse-button-1 and move mouse vertically to alter the contour level.
• ROI Annotation sets - create sets of annotation and allow ROI annotation to be set by selecting an item from a list.
• ROI Totaliser now counts up the number of 3-D connected regions and gives the total number of VOIs, and also (when producing a text or PDF report) produces sub-totals for ROIs categorised by annotation or by colour.
• Stand-alone program Roivol can now calculate ROI statistics separated by ROI colour and by annotation.
• New cost functions for image registration - normalised correlation and correlation ratio.
• Can now rotate images in the Image Resampler.
• On-screen rendering can now use different types of interpolation, when interpolation is turned on: bi-linear by a factor of 2, then nearest-neighbour; bi-linear up to native screen resolution; bi-cubic up to native screen resolution. Value at startup is set in user preferences. Button to toggle between different types of interpolation in image display frames.
• When displays are linked, the Master-Slave display relationship can now be made either with Slaves following the Master, or bi-directional with the Master also following the Slaves.
• Can launch tools and common dialogs from command-line invocation of Jim. From the command line, type:
  Jim --help to see the options.
• Axial and radial diffusivity maps in diffusion tensor analysis / tractography tract statistics.
• User can add CT presets. Jim detects CT data, and on loading a new CT image select the CT window that was last used.
• New option (-ver or --version) to show build version and build date from command-line. Available for all programs.
• When a single slice is selected, double-clicking on the slice with the shift key depressed, results in all slices being shown.
• Cord finder now allows the restriction of the slice range for outputting ROIs.
• DimChanger can now convert a single 3-D image into a 4-D image with multiple frames.
• New Image Filter in Image Resampler tool, allowing the separate colour components of a colour image to be arbitrarily manipulated.
• In all places where a user can choose a colour mapping (Image Overlay, Orthogonal planes in 3-D viewer etc), there is also the ability to invert the colour mapping.
• Reference Image slice positions can now be shown on the main image.
• Query/Retrieve tool supports C-MOVE (in addition to C-GET) for DICOM Query/Retrieve via settings in user Preferences.
• Screen shots can be made of graphs plotted in Graph Dialogs.
• New way of handling arterial input functions - any AIF with any time base can be used. AIF file contains 2 columns of data - time and plasma concentration values, and the time of arrival is the first time point at which the concentration rises above zero.
• Arterial input function resampling tool to allow an AIF collected with one time resolution to be resampled to a different time resolution for use with another image dataset.

These features are on top of those of Version 6:

• 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 text-mode Roivol program - calculates Region-of-Interest statistics from an ROI file.
• New 'Dynamic 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 all 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.
• 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^TM 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".
• For Fuzzy Connector, fuzzy threshold, and connectivity in 3-D are recorded in the ROI file generated.

These features are on top of those of Version 5:

• 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.

These features are on top of those of Version 4:

• Fuzzy Connector tool. Isolate image features based on their "fuzzy connectedness" in multi-parametric image space.
• 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^TM 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.

These features are on top of those of Version 3:

• 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.

Usability features:

• 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.

Image handling features:

• 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^TM images in both big-endian and little-endian format - completely transparently.