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ReleaseNotes.txt
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======================================
InsightSNAP (ITKGray branch) Release Notes
Version 1.6.0.1
(ITKGray branched from ITK-SNAP on 2008.07.31.)
======================================
The ITKgray patch addes the following features to ITKSnap:
* support for non-integer input images
* floodfill paintbrush mode
* topology checking tools
* undo/redo can be accessed from the menu
-----------------
1. New Features
-----------------
1.1. New in Version 1.6.0.1
---------------------------
1.1.1. Bug Fixes
- Major bug in release 1.6.0 involving disabled cursor movement in snake
segmentation mode has been resolved.
1.2. New in Version 1.6.0
-------------------------
1.2.1. 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
1.2.2. Bug Fixes
- Various bugs have been fixed :)
1.2.3. 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
1.3. New in Version 1.4.1
-------------------------
1.3.1. 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.
1.3.2. 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
1.3.3. 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
1.4. New in Version 1.4
-----------------------
1.4.1. 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.
1.4.2. 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!
1.4.3. Programmatic Enhancements
- SNAP and IRIS now share the sameset of OpenGL windows. This should prevent
crashes on some platforms.
1.4.4. Other
- SNAP available as a universal (Intel/PPC) binary for MacOS at itksnap.org
1.5. New in Version 1.2
-----------------------
1.5.1. 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.
1.5.2. 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.
1.5.3 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.
- The ability to export level set segmentation results as meshes or as floating
point images.
- Ability to use different color maps in automatic segmentation mode.
- Proper NIFTI coordinate transforms