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ITK-SNAP Release Notes - Version 4.2

Version 4.2.0 alpha.3

New Features

  • Experimental support for free rotation of the main image (Tools->Image Free Rotation...)
    • Polygon and paintbrush tools can be applied from oblique rotation angles
  • Native support for 32 and 64 bit floating point images
    • Previously, these images were represented internally as 16 bit integer, with rounding errors
    • NaN (not a number) values are supported, custom color can be assigned in the color map
  • Performance improvements:
    • Faster image load times made possible by efficient computatation of histogram and quantiles using the tdigest data structure
    • Faster rendering of large 2D images
  • Image IO Improvements:
    • NRRD Volume Sequence Reading
    • 4DCTA auto format detection now can detect wider range of images
  • Improvements to label definitions file IO:
    • A new submenu (Segmentation->Label Definitions includes recent items submenu)
    • Label definitions can be loaded by drag & drop
  • New commands for reloading image layers (in context menus and layer editor):
    • Main image and overlay can be reloaded from disk without closing the workspace
    • 4D (3D+time) images can be reloaded as multi-component images and vice versa
  • Added options to compose and invert transforms to the "open transform" dialog in the registration panel
  • Added a hotkey to switch between background & foreground labels
  • Added a hotkey to toggle continuous update of 3D rendering
  • More accurate UI text for loading/saving 3d/4d segmentations in 4d workspace
  • Multiple segmentation images can be loaded from the command line
  • Workspace tool itksnap-wt includes new commands for mesh layers

Bug Fixes

  • Closing main image from layer context menu now will correctly prompt saving changes for overlay layers
  • Loading 3d segmentation into a 4d time point no longer prompts warning, if the time point does not have unsaved changes
  • Now correctly displaying deformation grid for image layers displayed on top of main image

Version 4.0.2

Bug Fixes

  • Fixed an issue reporting invalid vector error when reading dicom series containing multiple images for only one slice
  • Fixed an issue caused long reading time when drag&drop large image files
  • Fixed an issue caused crash when using hotkeys < and > to change foreground labels

Version 4.0.1

Bug Fixes

  • Interpolation Dialog now displays correct initial settings
  • Reorient Dialog now correctly renders the axes direction when determinant of the direction matrix is negative
  • Registration panel now reslices 4D moving images into 4D

Version 4.0.0

New features

  • New VTK-based slice rendering logic
  • New build for Apple silicon
  • Support for 4D images
    • UI support for the 4th dimension
    • New Time Point Properties for 4D images
    • New 4D playing feature
  • Support for Volume Rendering in the 3D window
  • Support for loading and displaying external meshes into workspace
    • Now external VTK, VTP polydata meshes can be loaded into workspace
    • Support for mesh series loading into a 4D workspace
    • Color rendering for point and cell data
    • Adjustable contrast and color map for each data array
    • Rendering separate components or magnitude for vector arrays
  • Segmentation Meshes now have dedicated layer row in the Layer Inspector
  • Support for following image formats
    • Echo Cartesian Dicom
    • 4D CTA Dicom Series
    • MINC
  • Added Color Legend in the 3D window
  • Redesigned Slice View Layout Page in the Preference Dialog
  • Now mesh scene can be exported in STL format
  • Added orientation code in mesh export for 3D Slicer reading. (More info: https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/Slicer#Slicer_5.0:_Models_are_saved_in_LPS_coordinate_system_by_default)
  • New Multi Label Smoothing Tool
  • New Dark Mode Appearance
  • Updated library references to ITK 5, VTK 9, and Qt 6

Version 3.8.0

This version introduces an exciting new feature: the Distributed Segmentation Service (DSS). This service allows developers to make various image segmentation algorithms available to you directly in ITK-SNAP. Several algorithms have already been made available: most of them focused on hippocampus segmentation, and we expect more to appear soon. DSS is a web-based system, so data is sent to a server and processed by algorithm providers using their own computer hardware.

New features

  • New GUI for the DSS, under Tools->Distributed Segmentation Service
  • New support for multiple segmentation layers (switch between them with {,} keys)
  • Command-line functionality for interacting with the DSS service as a user or developer, part of itksnap-wt workspace editor tool
  • New functionality for plotting time-course data in the Image Information dialog
  • Implemented support for reading DICOM data with multiple images per z-position
  • Registration interface has improved image resizing support, support for flipping
  • Command-line tools c3d and greedy now can be installed using Help->Install Command-Line Tools
  • Support for reading "Generic ITK Images" in the "File->Open" dialog, makes it possible to open any image that ITK can read

Bug Fixes

  • Fixed crashes that occurred occasionally when loading multiple images with different orientations
  • Enabled loading of any image file supported by ITK via "Generic ITK" option in IO dialogs
  • Fixed crash when canceling random forest segmentation
  • Fixed crash when loading images of type char
  • Fixed issue with segmentation labels not resetting when loading a new image
  • Keyboard shortcuts Ctrl-1 to Ctrl-5 for loading recent images restored

Version 3.6.2

The main change in this version is the addition of the workspace building tool itksnap_ws. This tool will form the basis of the distributed segmentation system in ITK-SNAP.

  • Added tool itksnap_ws (in Utilities/Workspace)

Version 3.6.0

The main focus of this release is on making it easier to work with multiple images that have different size and resolution. This is particularly useful for viewing and segmenting MRI studies, where a single session contains many scans with different parameters. Important new features include the ability to load multiple images of different dimensions, voxel size, and orientation into a single ITK-SNAP window; automatic and manual registration; and enhanced support for DICOM format images. With these new features, researchers who work with MRI DICOM datasets will find it much easier to incorporate ITK-SNAP into their workflow. Another important new feature in this release is the ability to interpolate segmentation between slices. This makes it possible to create manual segmentations much more quickly than before.

New features

  • Multiple images with different dimensions, voxel size, and orientation can be visualized in the same ITK-SNAP window. When additional images are loaded, they are represented in memory in their native resolution, and resampled on the fly to match the screen resolution.

    • This means that you can use information from two MRI modalities to guide manual segmentation. You can load a T1-weighted image with 1.0mm isotropic resolution and a T2-weighted image with 0.4mm x 0.4mm x 2.0mm resolution, and use the full information from both of these images for your segmentation.

    • The manual segmentation is still performed in the voxel space of the main image.

  • A new registration tool is available under Tools->Registration. The tool provides both interactive manual registration and automatic affine and rigid registration.

    • Manual registration includes rotation/translation/scaling widgets and a mouse-based interactive registration mode, where moving the mouse over the 'moving' image performs rotation and translation. Rotation is performed by turning a 'wheel' widget, and very small rotations are possible. The center of rotation can be set by moving the cursor.

    • Automatic registration is quite fast. It allows rigid and affine registration. It supports mutual information (inter-modality) and patch cross-correlation (intra-modality) metrics. Optionally, a mask can be provided, over which the metric is computed. It is easy to generate masks using the segmentation interpolation tool (see below). Masks are useful when the extent of the images is different, e.g., one includes neck and another does not.

    • Registration results can be saved as matrix files compatible with ANTS, Convert3D and Greedy tools. Using Convert3D, they can be converted to FLIRT-compatible transform files. Registration results are also automatically saved in workspace files. Images can also be resliced into the space of the main image.

  • DICOM functionality is greatly improved.

    • After you load a 3D volume from a DICOM image directory, you can load other 3D volumes in the same directory quickly using the new File->Add Another DICOM Series submenu.

    • Listing of DICOM directories (in the Open Image wizard) is much faster than before. This really makes a difference when opening images on DVDs and USB sticks.

    • Dragging and dropping a DICOM file onto the ITK-SNAP window on Windows and Mac now shows the list of 3D volumes in the directory, allowing you to choose a volume to open.

  • A new tool for interpolating segmentations between slices under Tools->Interpolate Labels.

    • For images with thin slices and gradually changing anatomy, you can segment every fifth slice and fill in the missing slices using this new tool. Details of the algorithm are provided in an Insight Journal article. Interpolation can be performed for a specific label or for all labels.

  • Label visibility can be changed 'en masse' in the Label Editor, i.e., you can make all labels visible or hidden. This helps find a label in segmentation with many labels that occlude each other.

  • A new ''grid'' mode is provided for visualizing displacement fields. Displacement fields in formats used by ANTS and Greedy are currently supported.

  • The user interface automatically scales to reasonable size on very high DPI displays, such as the Miscrosoft Surface (tm). Environment flag QT_SCALE_FACTOR can be used to override.

Programmatic Enhancements

  • ITK-SNAP now includes Convert3D and Greedy registration tools as submodules. This is already used to support registration functionality, but in the future we will be adding more Convert3D-based functionality, such as filtering, etc.

  • The ImageWrapper class includes a dual slicing module that selects between orthogonal and non-orthogonal slicing based on image orientation. This is significantly cleaned up relative to earlier versions.

  • ITK-SNAP now compatible with Qt 5.6, which is the standard for the next 3 years

Bug Fixes

  • Fixed issue with Workspace->Save As... where you would be asked to save the current workspace (thx Laura W).
  • Fixed issue where DICOM data was not loading correctly when workspace was moved in the filesystem (thx Vincent F).
  • Fixed issue with loading of NRRD images on some systems due to non-US locale (thx Johan B)
  • Fixed behavior of Ctrl-W, so that when there are open dialog windows this keystroke closes them rather than the current image layer (thx Karl B)
  • Fixed issue with multi-component images, where every 100th component showed up as 'Magnitude' (this Phil. C)
  • Fixed OpenGL rendering issues on Windows 10 on some cards
  • Fixed computation of zoom factor on Retina displays
  • Fixed behavior of File Save browse dialogs on MacOS when saving .nii.gz files
  • Fixed issues with unnecessary prompting to save segmentations
  • Improved OpenGL compatibility, particularly in VTK-managed windows
  • Fixed issues with images >4GB not opening on Windows. This requires building ITK with ITK_USE_64BITS_IDS=TRUE
  • Fixed problems with histories not showing up in file dialogs
  • Fixed bug where scalpel tool did not work for anisotropic images
  • Several other fixes for specific crashes.

Known Issues

  • Some advanced features (label editor advanced tools, window shrinking) have not yet been ported to Qt. They will be ported in future versions, and expanded in the process. There is a plan to integrate SNAP and C3D which will provide much richer image processing support for images and segmentations.

  • The cutplane in the scalpel tool is too big when the camera is zoomed in and it needs a flip button. Also with dark labels you can't see the handle.

Version 3.4.0

This release was largely focused on improving the user experience through extensive changes to the GUI. We made access to the new features introduced in versions 3.0 and 3.2 more intuitive. The loading and display of multiple images has been extensively reworked and improved. In addition, we made the classification mode in the semi- automatic segmentation workflow more powerful by providing additional image and geometric features that the classifier can use to learn the patterns of difference between the classes labeled by the use. We have been alsobusy working on new functionality such as image registration within SNAP, and a smaller memory footprint, but these will become available in the 3.6 release. The main focus of 3.4 is on usability.

New Features

  • The controls for selecting segmentation labels have been brought back to the main SNAP panel, where they were in versions 1 and 2. This will make the interface more familiar to long-time users.

  • The interface for loading and viewing additional image layers has been extensively redesigned. When more than one anatomical image is loaded into ITK-SNAP, the default behavior is to display one image at full size and the rest of the images as thumbnails. Clicking the thumbnails makes them full size. This new thumbnail mode is far more intuitive for working with multiple images than the method of semi-transparent overlays employed in previous versions.

  • The IO dialog for opening additional images promts whether the user would like the image to be shown side by side with an existing image or as a semi-transparent overlay.

  • The thumbnails have a context menu button that provides fast access to common image commands, such as adjusting contrast and color map.

  • The tiled display mode introduced in version 3.0 is also available as an alternative to the thumbnail display.

  • The new thumbnail mode makes semi-automatic segmentation easier to work with because one can switch easily between anatomical images and the speed (blue and white) image during pre-segmentation, bubble placement and contour evolution.

  • A new image annotation tool has been added to the main tool palette. This tool can be used to measure distances on image slices, draw lines, measure angles between lines, and place text annotations in specific points in the 3D image. Annotations can be exported and imported, allowing teams to comment on medical images and segmentations. Annotations are automatically saved in workspace files.

  • Command tooltips have been redesigned and now include information on the shortcut key to activate each command. In addion, tooltips for the tools in the main palette describe the actions of each mouse button. Many new shortcuts have been added.

  • Cleaned up the behavior of mouse buttons and mouse scrolling to be more consistent between modes. Added Shift-scroll action, which scrolls through timepoints in a 4D image and components in a 3D multi-component image.

  • Added the ability to generate "contextual" features in the classification mode in the semi-automatic segmentation workflow. Two types of contextual features are provided: neighboring intensity features, and coordinate features. The former allow the classifier to learn patterns of textural differences between regions in the image. When used, the classifier can separate regions that have identical average intensity but different texture. The coordinate features allow the classifier to learn geometrical information, such as the location/extent of the structure of interest relative to the background structures. This can be used to segment a structure that has no intensity contrast with adjacent structures, simply by giving the classifer hints as to the location of the boundary on a few slices. These new features are available by pressing "More..." when in classification mode.

  • Added some extra controls when working in classificaiton mode, such as setting the forest size and tree depth for the random forest classifier and a slider for "classifier bias", which allows you to bias the classfier output more toward the foreground class or background classes.

  • Added the ability to select more than one class as the foreground class in the random forest classification mode. This is powerful when the foreground object has heterogeneous intensity.

  • Training examples drawn in random forest classificaiton mode are now retained and can be reused to label multiple structures.

Programmatic Improvements

  • Refactored the software to allow multiple images that occupy different anatomical space to be loaded in the same ITK-SNAP session. This functionality has not yet been enabled, and will be rolled out it 3.4 as part of the new image registration functionality.

  • Updated to Qt 5.4

  • Fixed font size and other rendering issues on Retina displays. Added high-resolution icons for Retina.

  • Made it possible to build ITK-SNAP against older Qt version 4.8. In some Linux environments, applications based on Qt5 do not work well over remote connection (ssh -X, VNC, x2go, NX) because the way Qt and X11 interface was changed drastically in Qt5. The fallback to Qt4 makes it possible to run the new SNAP version in cluster environments.

  • Fixed problems with loading images > 4gb

  • Restored ability to build on 64 bit Windows

Version 3.2.0

The main new feature introduced in this release is supervised classification. The release also is built against Qt5 (3.0 used Qt4.8), which resulted in a lot of changes to compilation and packaging. Quite a few bugs have been fixed and the release should be more stable than 3.0.

New Features

  • Added a supervised classification presegmentation mode. This mode allows the user to compute the speed image by marking examples of two or more tissue classes in an image with the paintbrush or polygon tools. The mode works with multi-component data and multiple image layers.

  • Redesigned the semi-automatic segmentation GUI to be simpler to use. Now the presegmentation can be done without bringing up a separate dialog. Also the speed image is immediately computed for most presegmentation modes. Overall, semi-automatic segmentation should be much easier to use than in the past.

  • ITK-SNAP can now read 4D datasets. Previously such datasets would have to be converted to a multi-component 3D dataset by the user. Now working with dynamic datasets is much easier.

  • Added a label palette control for faster selection of labels

  • Added a 'flip' button for the 3D scalpel tool

  • Added support for syncing camera state between multiple SNAP sessions

  • Significantly improved behavior of open/save dialogs throughout the code. All dialogs now use the same code and open in a sensible place.

  • Added option to auto-adjust image contrast on load

  • Improved volumes & statistics computation speed and display formatting

Bug Fixes

  • Fixed a bug with small bubbles not growing in snake mode.

  • Refactored the DICOM input code and fixed several errors in the process.

  • Fixed numerous problems on Retina displays

  • Modified the clustering code to use Eigendecomposition for increased robusness, particularly when applied to binary and multi-label images.

  • Fixed several dozen smaller bugs

Programmatic Improvements

  • Migrated to Qt5 as well as up to date versions of ITK (4.5) and VTK (6.1)

  • Added scripted GUI testing functionality. This allows interactions to be recorded and played back on different platforms and is great for regression testing. Four tests are in this release, and more will be developed soon.

Version 3.0.0

This is a major new release of ITK-SNAP. The user interface has been completely rewritten using the Qt platform, and new functionality for multi-modal image segmentation has been added.

New functionality for multi-modality image segmentation

  • SNAP is no longer limited to just scalar-valued and RGB-valued images. An image with any number of components can be loaded into SNAP. The GUI provides widgets for selecting the currently shown component, deriving scalar images from the components (magnitude, maximum, average), and for three-component images, rendering them as color RGB images. It is also possible to animate components, e.g., for time-varying image data. Multi-component images enjoy access to the same features as scalar images, such as curve-based contrast adjustment, colormaps, etc.

  • When multiple layers are loaded into SNAP, the user has a new option to tile the layers in each of the 2D slice views. This greatly simplifies working with multiple overlays. This also carries over to the automatic segmentation mode, where the speed image can now be displayed side by side with the anatomical images. It can also aid manual segmentation of multi-modality data. During manual segmentation, polygon outlines are traced on top of each of the tiled views.

  • Automatic segmentation (using active contours) can now be performed in multi-modality images. Multiple image layers, each of which may have multiple components (e.g., RGB, complex or tensor data), can be passed to the auto-segmentation mode. Once there, the user can use the new clustering preprocessing mode to derive a speed image from this multi-variate input. The current implementation of clustering uses Gaussian Mixture Modeling. The user selects the desired number of clusters (i.e., tissue classes) and once the clusters are initialized, chooses the cluster of interest.

New features in the Qt-based GUI

  • The graphical user interface (GUI) uses Qt, a much more powerful toolkit than the FLTK toolkit in the previous versions. The new GUI is much richer with multiple access paths to common functions (such as choosing the active label or changing the color map for an overlay). There are fewer 'apply' buttons to press, as most of the time, the program reacts immediately to user input into the widgets. More features are available in the left-side panel, and these features are organized more logically than before.

  • New functionality for saving and opening workspaces. A workspace represents the state of ITK-SNAP at a given moment, including all the images currently loaded in an ITK-SNAP window, as well as associated settings and parameters. Workspaces are saved in the XML format. They can be packaged together with the images to which they refer and shared with other users.

  • The layer inspector dialog is greatly improved, with new features for reordering layers, quickly changing their visibility, applying a colormap, adjusting contrast, saving, etc. The speed image and level set image, created by the program during automatic segmentation, are now accessible in the layer inspector, so the user can change their color maps as well. In the future, the layer inspector will provide access to much more functionality, such as applying image processing operations (smoothing, feature extraction, bias field correction) to individual layers.

  • The various plots in the GUI now use the vtkChart library in VTK. This provides richer visualization capabilities than the old version in which all the plots were rendered using custom OpenGL code. This is particularly noticable in the contrast adjustment page of the layer inspector and in the preprocessing dialog in auto-segmentation mode.

  • The window shown at startup shows a graphical list of recently opened images and workspaces. This makes it easier to quickly load an image, and keeps the GUI clean during startup.

  • SNAP recognizes pinch gestures (tested on the Mac) for zoom. This should make interaction easier for trackpad users.

  • Layers can be assigned nicknames, such as "T1".

  • Unicode support. Filenames and user-entered data can now be in any language.

  • The label editor has new features, such as resetting all labels do defaults, filtering labels by name, assinging foreground/background labels directly from the dialog.

Improvements to 3D rendering window

  • The 3D rendering window now uses the VTK toolkit for rendering. This will make it easier to introduce new functionality (such as volume rendering) in future versions.

  • The 3D rendering pipeline is much smarter than before. It detects changes to individual labels in the segmentation, so each paint operation no longer requires the entire set of 3D meshes to be recomputed. Rendering is significantly faster than before.

  • There is a new option to automatically render meshes in a background thread. When enabled, the mesh updates itself in response to polygon and paintbrush operations. This works well even for large and complex segmentations. However, this is still an experimental feature and may lead to occasional weird crashes due to multi-threading issues.

  • The scalpel tool uses VTK's 3D cutplane widget that can be rotated and moved after the cut has been drawn.

Other new features

  • Reduced memory footprint for large images. The previous version of SNAP would allocate on the order of 6 bytes for every voxel in the main image. Two bytes were used to store the grayscale image intensity, two for the segmentation, and two for the segmentation undo buffer. The undo buffer is now stored in a compressed format, reducing the required memory by almost one third. In the future, we also plan to compress the segmentation itself, which will cut the memory use by another 2 bytes per voxel.

  • Improved support for reading/parsing DICOM data. When the user opens a file in a directory containing DICOM images, SNAP parses this directory much faster than in previous versions (especially when data is on CDs) and lists all the series with their dimensions and other meta-data, making it easier to determine which series one wishes to load.

Programmatic improvements

  • The SNAP code has been extensively refactored. There is a new "model" layer separating the Qt GUI from the "logic" layer. This layer is agnostic to the type of GUI toolkit used, and implements generic GUI logic. This design minimizes the amount of Qt code, so that swapping Qt versions or even porting to a different toolkit will be easier in the future. Unlike the old FLTK code, which had huge numbers callbacks, the new code relies on a widget-model coupling mechanism. This makes the code more robust and reduces the amount of Qt-aware code.

Version 2.4.0

This is the last planned release of the FLTK-based version of ITK-SNAP. It adds minimal new functionality and addressed a number of bugs reported in the last year. The subsequent releases of ITK-SNAP will be based on the Qt platform and will have the 3.x version number.

New Features and UI Improvements

  • Ported the dependency on ITK 3.20.1 to ITK 4.2 on all operating systems: Mac OS X, Linux, and Windows.

  • ITK-SNAP can read and write MRC images now.

Bug Fixes and Stability Improvements

  • Fixed a problem with the RAI code which was not updating after reorienting.

  • Fixed bug ID: 3371200: The saving of the preprocessed image was failing.

  • Fixed bug ID: 3309784 and 3415653: Windows file browser broken and enable all document setting not available in version 2.2.0.

  • Fixed bug ID: 3415681 It was not possible to update the mesh when working with volumes of one slice. An exception is thrown and catch with fl_alert.

  • Fixed bug ID: 3323300 BYU mesh saving was save-able, while the internal data was not prepared for this saving. The user interface is correctly updated now. In addition, the BYU writer save geometric data as well.

  • Fixed: bug ID: 3023489: When running from command line with -o flag, there was no check to see if images are same size. Two asserts were changed in exception throwing.

  • Fixes for building with different releases of fltk 1.3.

  • Corrected a bug in the code with SparseLevelSet filter being used instead of ParallelSparse.

Version 2.2.0

This is largely a maintenance release, with a few usability enhancements based on user feedback. The main change programmatically is 64 bit support on Linux, MacOS and Windows.

New Features and UI Improvements

  • 64 bit versions of the software are available for Linux, Windows and Mac. These versions are now built nightly and will be distributed on SourceForge.net. For this to work, we had to change to newer versions of the supporting libraries: ITK 3.20, VTK 5.6.1, and FLTK 1.3.0.rc3. The latter was necessary for 64 bit MacOS, which many users have requested. Thanks to Michael Hanke for providing a patch for ITK 3.18 compatibility.

  • The maximum number of labels has been increased to 65535 to support interoperability with tools like FreeSurfer, which generate segmentations with large numbers of labels.

  • A new window for displaying volumes and statistics. Previously, users had to export volumes to a text file in order to view them. Now they can be viewed dynamically. This was possible by moving to FLTK 1.3, which includes the Fl_Table widget.

  • A new tab on the layer inspector displaying image metadata, particularly useful for DICOM files.

  • Several changes to the polygon drawing interface. The buttons at the bottom of the slice window are now shown dynamically, based on what the user is doing. Right clicking brings up a popup menu, allowing to bypass the edit mode if desired. An 'undo point' operation is provided.

  • Users can change the appearance of the polygon drawing UI elements. This addresses the request to get rid of the dotted line closing the polygon.

  • Intensity window and level in the image contrast dialog are no longer clamped by the minimum and maximum intensity in the image. This is useful for displaying statistical maps, where a certain fixed output range is desired.

  • Finally implemented all the options under Segmentation->Export as Mesh. You can now export meshes for all labels either as separate mesh files or as a single scene. The latter is recommended with the VTK mesh format, where the label ids of the meshes are preserved.

  • Collapsable slice windows. The new 'collapse' button gets rid of the UI and just shows the selected slice. This is useful when you have multiple SNAP sessions open at once. SNAP can be opened in this mode using the new command-line option '--compact ', where is 'a' for axial, 's' for sagittal or 'c' for coronal. You can restore default SNAP layout using Ctrl-F3 (Command-F3 on the Mac) or using the toolbar button that pops up.

  • Also added command line options --zoom and --help

  • The 'reset view' button under the slice windows has been renamed 'zoom to fit' and it behaves more sensibly when zoom is linked across the slice views.

  • Improved integration with MacOS and Windows operating systems. On both MacOS and Windows, you can drag and drop a file into an open SNAP window and you will be prompted to open that file as a grey image, as a segmentation, as an overlay, or as a grey image in another SNAP session. Additionally, on the Mac, you can drag and drop files to the SNAP icon on the Dock, even if an SNAP session is not running.

  • Added an option under File menu to open a new SNAP session.

  • Ability to save segmentation mesh in active contour mode

Bug Fixes and Stability Improvements

  • Fixed a problem with certain operations being very slow because of the way the progress bars were displayed. Preprocessing, mesh rendering and mesh IO will now be much faster

  • Fixed problems with the snake parameter dialog. The images are now properly displayed and animation works.

  • Fixed problems with automatic panning in crosshairs mode. Also added a button to enable this feature; it is disabled by default.

  • Changed defaults for edge-based snakes to have non-zero weight

  • Fixed display issues on newer MacBook Pro

  • Fixed problem with bubbles not being spherical for certain image orientations

Version 2.0

New Features and UI Improvements

  • Support for multiple image layers. Users can now load gray and RGB images as overlays on top of the main image layer. For example, one can display a statistical map as an overlay over an anatomical image. As of version 1.9.8, overlays must have the same dimensions as the main image.

  • A new layer inspector window. Each layer in SNAP (main image and each of the overlays) can be examined using the layer inspector. Currently there are three tabs: one for setting the intensity mapping of the layer (i.e., mapping from image intensity to display intensity); one for selecting and editing the color map and transparency of the layer; and one providing information about the layer. The layer inspector replaces the old "Image Information" and "Intensity Curve" windows. The color bar editor is only partially functional as of 1.9.9.

  • Hiding the UI. Using the 'F3' key, users can toggle certain user interface elements on and off. Press 'F3' once, and the left sidebar and the menu bar disappear. Press 'F3' twice, and all the UI elements disappear, so you are looking just at the image. Press 'F3' again, and the UI is restored to the original state. This feature works well with the '+' buttons on the slice windows. It's intended for multi-session SNAP users, so that the screen real estate can be used more efficiently by multiple SNAP sessions.

  • Because now the most common SNAP commands have a shortcut, you will be able to do a lot with the UI hidden. Select 'Help->Keyboard Shortcuts' to see a listing.

  • Fullscreen mode. Press 'F4' to toggle fullscreen SNAP. Use it with 'F3' to let the image occupy the whole screen.

  • An expanded menu bar. We have split the menu into File, Segmentation and Overlay menus to provide easier and faster access to the ITK-SNAP features.

  • Native file chooser. On Windows and MacOS, ITK-SNAP will use a native file chooser instead of the FLTK built-in file chooser. On Mac OSX, the native file chooser can be further enhanced by installing the DTI-TK Quick Look plugin that supports NIfTI/Analyze image preview (www.nitrc.org/projects/dtitk)

  • When launched from command line, SNAP can automatically determine whether an image is a 3-component RGB image or a grayscale image. To use this functionality, users must run SNAP without "-g" or "-rgb" options:

    itksnap image.nii

    This feature is ideal for users who want to associate ITK-SNAP with certain 3D image types in their operating system (in Finder or Windows Explorer).

  • Automatic check for software update. Users can enable automatic update checking.

  • External web browser support. Help and other HTML pages are now displayed in the operating system's own web browser, from itksnap.org. This may displease users connected to the internet, but this makes managing documentation a lot easier and hopefully will allow us to keep the documentation up to date with the features.

  • Crash recovery. When an out-of-memory or other crash occurs, ITK-SNAP will ask you if you want to save the segmentation image before exiting. Of course this may not always work, but it should make a lot of frustrated users a little less frustrated.

  • Reduced the memory footprint. There is still room for improvement, of course. Currently, ITK-SNAP requires 6 bytes per voxel in manual segmentation mode. More memory is needed for mesh rendering, and a lot more for automatic segmentation. When loading images in 32-bit or 64-bit formats, more memory may be required at the time of image IO. That is because ITK NIFTI reader (and maybe other readers) keeps a second copy of the image in memory during IO. This memory is immediately deallocated though.

  • Unified navigation modes. The crosshair mode allows zoom and pan (RMB/MMB), and has an auto-pan feature when you move the crosshair close to the edge of the slice window. The zoom/pan mode is redundant, but we left it in place for backward compatibility. In the zoom/pan mode, zoom is RMB, pan is LMB, crosshair motion is MMB. In all other modes, crosshair motion is accessible through MMB as well.

Bug Fixes

  • Fixed an issue with SNAP reading certain types of image twice from disc. This should speed up the reading of floating point images, for example.

  • Color map cache is now computed on the fly. This makes interaction with the intensity curve and color map more real-time.

  • Found a problem where in Release mode, the active contour would do nothing. Did not know how to fix it correctly, so replaced the parallel sparse field solver with the non-parallel one. This may slow down automatic segmentation on some machines, so this is an outstanding issue.

  • Found a bug that caused images with unusual coordinate orientations to be incorrectly displayed (wrong coordinate labels assigned). This was caused by incorrect mapping of ITK direction matrix to "RAI" codes in SNAP. This affects display of NIFTI, DICOM and other image files. It also affects the behavior of the Reorient Image dialog.

  • Please see the bug tracker on itksnap.org for the full listing of bug fixes.

Website Changes

  • The itksnap.org website has been Wikified. Content can now be edited on the fly.

Version 1.8

New Features and UI Improvements

  • Support for reading floating point images of arbitrary range. SNAP still represents gray images internally as signed short, but now it can load a floating point image and remap its intensity range to signed shorts. When displaying intensity values, it will map back to float.

  • A new 'Adaptive' paintbrush. Under the paintbrush tool, it can be selected using the 'Shape' drop down. This tool can speed up manual segmentation quite a bit for some users. This brush has the shape of a rectagle. As you click on a pixel in one of the slice views, the brush will fill a region that includes the pixel you clicked and has more or less uniform intensity. For example, in brain MRI, if you click in the ventricles near the caudate, the brush will fill the ventricle but not the caudate. This is not as powerful as running the level set segmentation, but it's very local and great for quickly segmenting structures - or dealing with inhomogeneities. The underlying algorithm is ITK's watershed segmentation. You can control the tolerance of the adaptive brush ('granularity' input, lower values produce smaller, more cohesive regions). The brush can be used in 2D or 3D.

    This feature was inspired by a similar tool in ITKGrey, a tool from the Vista Lab at Stanford that itself is a branch of an older version of ITK-SNAP. Let us know if this feature works for you. Potentially, we may add other algorithms in the future, including running the level set inside of the brush.

  • Support for image orientation. This is a major step towards NIFTI compatibility (part of our R03 effort) and something many users should find helpful. Formats such as NIFTI, DICOM, and a couple others encode the orientation of the image axes in patient space, and even allow image axes to not be parallel to the anatomical axes. SNAP now reads this information from the image header and uses it to assign anatomical labels and compute anatomical coordinates. One of the consequences of this change is that the image IO wizard no longer requires specifying an orientation code (e.g., 'RAI') when loading an image, since this information is read in the header.

  • A new 'reorient image' dialog has been added, so that if the orientation information in the header is wrong, you can change the orientation and save the image. For now, the user can only specify reorientations that are parallel to the anatomical axes.

  • World cursor coordinates (under image information) are now displayed in NIFTI / MNI coordinates as well as ITK coordinates. The difference is that the NIFTI coordinates incorporate orientation and are in the (L->R, P->A, I->S) coordinate frame. ITK coordinates are (x * spacing + origin), and ignore orientation.

  • 3D Meshes generated and rendered by SNAP are now represented in NIFTI world coordinates. Previously, the coordinates were computed using the formula

    x_mesh = x_voxel * spacing + origin

    In version 1.8 and beyond, the mesh coordinates are computed as

    x_mesh = nifti_sform_matrix * [x_voxel; 1]

    This means that the meshes output by earlier versions of SNAP may be translated and rotated relative to the meshes output by version 1.8. This will not affect users who simply view meshes in SNAP; however users who export meshes to other programs will be affected.

  • Multisession cursor (similar to yoking in MRIcro) now uses these NIFTI coordinates rather than ITK coordinates. This is a key feature because it enables users to work with MRI scans acquired during the same session with different orientations. For example, a coronal T1 scan and an oblique T2 scan can be loaded in two SNAP instances, and the cursor will be correctly linked across the two.

    CAVEAT: SNAP's cursor always falls on voxel centers. This means that the multisession cursor correspondence is not exact, but rounded to the nearest voxel. If in session A you move your cursor, the cursor in session B will move to the voxel center closest to the physical position referenced by the cursor in session A.

  • A new multi-session zoom feature. Similar to the multi-session cursor, this allows the zoom level to be maintained across multiple SNAP sessions. Useful if you do a lot of zooming in and out when working with a pair of scans. This is disabled by default and must be enabled in each SNAP session using the checkbox under the 'Zoom/Pan Tool'.

  • Changes to how zoom works, related to above. Now 'zoom views together' is on by default, meaning that the zoom factor is the same in axial, coronal and sagittal windows. Zoom level is specified in px/mm, where px is the number of screen pixels (in other words, a metric equivalent of dots per inch). Before, zoom was specified in percent, relative to an optimal zoom that would best fit all three windows. With the new way you have more control over the zoom. For example, if your image has 1mm voxels, you can have one to one correspondence between screen pixels and voxels by setting the zoom to 1 px/mm.

  • Multisession 3D views. When the multisession cursor is selected, the 3D views are also synchronized across sessions. This works even if the images opened in the two SNAP sessions have different dimensions, orientation and spacing. SNAP 3D window now uses NIFTI world coordinates, so as long as the two images overlap in world space, so will the 3D views of the two images. This feature is useful when comparing two segmentations of the same image.

  • A new ruler display in slice windows. Can be disabled or modified on the display options dialog.

  • Much better tracking of changes to the segmentation image and better promting to save changes before quitting or loading a new image. The title bar display is also improved and uses an asterisk to indicate unsaved changes.

  • The command-line options have been updated. You can now load a grey image without using any flags (e.g., itksnap image.nii) and there is a new '-rgb' flag for loading an RGB image from command line. The upshot is that you can now associate SNAP with image file extensions in the operating system and double-click an image file to open it in SNAP.

  • A new 'Tools' dialog on the label editor. This dialog is intended to provide several tools for merging or modifying labels. The first tool is to combine a pair of labels into one. Previously, this was possible using the 3D scalpel tool, but that was not really an intuitive way to relabel images.

  • As part of above, a new topological merge tool, developed by Nick Tustison, Brian Avants and Marcelo Siqueira (I hope I did not forget anyone). Given adjacent labels A and B, it will replace most voxels in B with the label A, while preserving the topology of A. This tool is used to preserve topology during manual segmentation. If A has correct topology and you want to add some region to A, label this region with label B, and then grow A into B with topology preservation. This is a work in progress, and feedback would be welcome on this feature.

  • Documented existing keyboard shortcuts and added some new ones. Available shortcuts can be listed by selecting Help->Shortcuts.

Programmatic/Distribution Changes

  • SNAP is now built against ITK 3.8, offering several improvements, especially in how image orientation is handled.

  • IPC communications (technology that allows multisession cursor and zoom) now has some versioning built into it, so if you are running two versions of SNAP, they will not clash.

  • On LINUX, we now distribute a .tgz archive instead of a script installer. Some people complained about the latter. We can also make .rpm and .deb packages although these won't be posted for public download yet.

1.7.3. Bug Fixes

  • Level set fix for ITK 3.8 fixes automatic segmentation's weird behavior

Version 1.6.0.1

Bug Fixes

  • Major bug in release 1.6.0 involving disabled cursor movement in snake segmentation mode has been resolved.

Version 1.6.0

New Features and UI Improvements

  • You can now save a sequence of all axial, coronal or sagittal slices with overlays as PNG files (File->Save->Screenshot Series).

  • Automatic window and level computation based on the image histogram. The window and level are set to the 1st and 99th percentiles of the intensity histogram, respectively. This is much more robust to hypo and hyper-intensity in medical imaging data. The feature is accessed in the "Options->Image Contrast" menu (or hit Alt-I in the main window).

  • Cursor synchronization across multiple SNAP sessions (similar to the Yoke feature in MRIcro). The mechanism uses POSIX shared memory. Can be turned off using the 'Synchronize Cursor' checkbox. Currently, only enabled in manual segmentation mode; probably will enable in snake mode in the near future.

    --- NOTE FOR MacOS Users ---
MacOS doesn't allow you double-click the application icon to open a
new instance. To open multiple instances of ITK-SNAP, you need to launch
it from the command line.
----------------------------

  • SNAP will prompt you before closing if there are unsaved changes.

  • A new 'New->Segmentation Image' menu item will clear the current segmentation.

  • Support for RGB (color) images in SNAP. This is great for segmenting in DTI data (manually, for the time being). RGB images can be loaded as the base image or as an overlay over the gray. To create these RGB images, use the new DTI-TK developed by Hui (Gary) Zhang, available from

    http://www.picsl.upenn.edu/resources_dtitk.aspx

  • Segmentations can be exported as VTK meshes (for example, for loading in ParaView).

  • Multilevel undo/redo functionality for all segmentation operations (polygon, paintbrush, freehand, 3D segmentation, 3D cutplane). Undo memory is preserved when loading new segmentation images.

  • Freehand drawing support in polygon mode (hold and drag the mouse button). This feature is especially useful for using SNAP on a tablet.

  • Added keyboard shortcuts 'a','s','d' for the opacity slider

  • Shortened/simplified some of the menu items

Bug Fixes

  • Various bugs have been fixed :)

Distribution Changes

  • SNAP website fully migrated to sourceforge.net

  • Mac Universal binaries supporting Intel and PCC, Tiger and Leopard are now available starting with 1.6.0

  • Linux binaries will be available starting with 1.6.0

Version 1.4.1

New Features and UI Improvements

  • Added paintbrush tool to the main toolbar. Paintbrush can be used to quickly touch up segmentations. Left mouse button paints with selected label, right button acts as an erasor

  • Went through and added/edited tooltips in the program to be more accurate. It should be easier to make sense of the program now

  • Added a menu option for saving the level set image during active contour evolution. This is an important feature because it allows users to save segmentations before sub-voxel accuracy is lost. In particular, this can be used in conjunction with ParaView to generate meshes from segmentations.

  • You can now save and restore the camera settings in the 3D view within a single SNAP session. This can be useful for generating screen shots of different segmentation from the same viewpoint. Press 's' in the 3D window to save the camera state and 'r' to restore it.

Bug Fixes

  • MAJOR: fixed bug that was causing crashes on Win32 during polygon drawing (thanks to Jeff Tsao for this bug fix!)

  • Fixed problems with the getsnap.sh linux script

  • Some menu items were enabled when they should not have been, now are disabled.

  • Rare bug where speed function very close to 1 was not being rounded correctly and may have caused crashes on some systems

  • Fixed problem where the screen was blank after loading preprocessed image

  • Fixed crash when changing bubble radius and then going back to preprocessing mode

Distribution Changes

  • Interim SNAP releases are now hosted on SourceForge. ITK repository will only be used to host major releases (like 1.6). This allows us to check stuff in independently of the ITK code freezes. It also makes it easier to add new developers.

  • SNAP CMake files should automatically detect when SNAP is being built outside of ITK's InsightApplications. This means you can build SNAP on it's own and the download size is reduced

Version 1.4

New Features and User Interface Improvements

  • New and improved label editor. You can easily switch between labels while in the editor and the interface for adding new labels is more intuitive. You can now delete labels.

  • New and improved interface for intensity reparameterization. The histogram display is more visible and you have more control over the number of bins in the histogram and the scaling of the bars (linear or log).

  • SNAP remembers all settings associated with loading an image. This means that any image loaded previously can be reloaded without going throught the wizard.

  • We've added File->Load Previous menu to let you load images quickly

  • SNAP can now read DICOM file series (experimental support) and it can read and write VoxBo CUB image files.

  • SNAP remembers more image-associated settings from session to session. For example, it will remember the intensity reparameterization that you last used. SNAP will also remember the orientation ("RAI" code) that was last used to read each image.

  • New Image Information window is available under the File menu. It displays the size of the image and the current cursor position.

  • A color map feature has been added in the automatic segmentation mode. The color map lets you select different color schemes for displaying the probability map / speed image.

  • Small improvements to the active contour 2D example dialog have been made

  • A progress monitor has been added for the 3D renderer in main SNAP window.

  • New buttons allow taking of snapshots in each of the SNAP image windows

  • The tutorial has been updated to reflect the new features.

Bug Fixes.

  • SNAP should crash a lot less than before

  • The Left-Right orientation should be correctly handled by SNAP. You still have to supply the correct orientation ("RAI Code") when loading the image.

  • The bug with the segmentation being shifted when using "Resample Region" option has been fixed

  • 3D window handles images with non-zero origin better

  • Initialization bubbles have been fixed to be floating point

  • Lots of other small bugs have been fixed!

Programmatic Enhancements

  • SNAP and IRIS now share the sameset of OpenGL windows. This should prevent crashes on some platforms.

Other

  • SNAP available as a universal (Intel/PPC) binary for MacOS at itksnap.org

Version 1.2

User Interface Improvements

  • The ability to switch between 4-view mode and single view mode. Each of the slice views and the 3D view can be expanded to occupy the entire SNAP window.

  • A zoom thumbnail is now displayed when a slice view is zoomed in. The thumbnail view can be used to pan the slice.

  • User can specify whether he/she prefers to start in linked zoom mode or in unlinked zoom mode.

  • User can change the appearance of various display elements, including the crosshairs, the region of interest selection box, the window background and more.

  • SNAP automatically determines the image orientation (RAI) when that information is available in the image file

  • SNAP remembers the last ROI used for each image.

Programmatic Improvements

  • The level set segmentation pipeline has been rewritten, taking advantage of the stop and go functionality of ITK finite difference filters. This means fewer unexplained crashes and simpler code.

  • A state-machine has been added to the user interface logic code. This machine automatically activates and deactivates UI widgets based on a set of flags. Rules such as Flag A => Flag B can be added to the state machine.

Bug Fixes

  • Slice views update correctly when the SNAP window is resized

  • Accepting a polygon now works for high resolution images.

  • Fixed a crash on some systems when running edge-based snake segmentation with an advection term.