ReleaseNotes.txt

======================================
 InsightSNAP Release Notes
 Version 2.2.0
======================================


-----------------
1. New Features
-----------------

1.1. New in 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.

1.1.1. 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 <axis>', where <axis> 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

1.1.2. 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

1.2. New in Version 2.0
----------------------------------------------

1.2.1. 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.
    

1.2.2. 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.
 
1.2.3. Website Changes

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



1.3. New in Version 1.8
----------------------------------------------

1.3.1. 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.

1.3.2. 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.

1.3.3. Bug Fixes

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

1.4. New in Version 1.6.0.1
---------------------------

1.4.1. Bug Fixes

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


1.5. New in Version 1.6.0
-------------------------

1.5.1. 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

1.5.2. Bug Fixes

 -  Various bugs have been fixed :)

1.5.3. 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


1.6. New in Version 1.4.1
-------------------------

1.6.1. 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.

1.6.2. 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

1.6.3. 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


1.7. New in Version 1.4
-----------------------

1.7.1. 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.

1.7.2. 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!

1.7.3. Programmatic Enhancements

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

1.7.4. Other

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


1.8. New in Version 1.2
-----------------------

1.8.1. 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.

1.8.2. 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.

1.8.3 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.


2. Known Issues
-----------------
 -  


3. Wish List
-----------------
 -  The ability to perform 2D level set segmentation in each slice view.