"Verpeilt compiled""No morning without warning"Author Contact:Ben Glocker
SUSI is a segmentation tool mainly for medical image data. It is developed for easy integration of new algorithms and rapid testing of prototypes. The GUI is based on FLTK 1.6. All rendering is done by the OpenGL library.
Existing Features
Import images
Meta Image Format (.mhd + .raw)
Analyze Image Format (.hdr + .img)
DICOM (based on the OpenSource DICOM library GDCM)
Export images
Meta Image Format (.mhd + .raw)
Analyze Image Format (.hdr + .img)
DICOM (based on the OpenSource DICOM library GDCM)
Image Processing
Transformation
Downsampling
Resampling (in resolution and physical voxel size)
Warping (rigid transforation)
Flipping
Rotating
Filtering
Inverting
Smoothing
Gradient filters
Histogram
Data Type Conversion
Segmentation
Methods
Thresholding
Region growing
Clustering
Graph cuts
Pre/Post-processing
Region of interest
Cropping
Rejoining
Inverting
Labeling
Combining segmentations
Erosion / Dilation
Boundary extraction
Skeleton extraction
Distance transformation (Chamfer distance)
Intensity replacement
Visualization
Slice view
Surface rendering (Marching Cubes) with OpenInventor export
Volume rendering
Misc
PET Attenuation map generation from CT image
Motion tracking & compensation
Diameter tracking
Recently Added
Diameter tracking (07.09.2005)
DICOM export (02.09.05)
Deletetion of brushes / Copy & Paste (Graph Cuts) (01.09.05)
Data type conversion (01.08.05)
Motion tracking & compensation (31.08.05)
3D gaussian smoothing (26.08.05)
Joining images takes dimensions, physical size and patient position into account (12.08.05)
Intensity shift by -1024 for unsigned short images (11.08.05)
Intensity replacement with HU Units for background voxels (05.08.05)
Analyze import from Big Endian systems (04.08.05)
Analyze Image Format for Import and Export (02.08.05)
Display of image information (02.08.05)
Information about the segmentation properties as dialog (size, volume, voxel numbers, etc) (02.08.05)
Cross-Hair in slice view (01.08.05)
Upcoming Features
Several logical operators for combining segmentations
Line profiles
Histogram operations
Filter settings dialog
Automatic dialog closing
Feature Requests
Bug reports
Open
Sometimes seg faults when closing the volume rendering dialog
Problems with exported OpenInventor models
Still bugs in ROI and rejoining (e.g. after downsampling)
Wrap-around effects in filters (gauss2d, mean2d, median2d, laplace2d, sobel2d, prewitt2d)
Resampling of single slices (2d,z=1) doesn't work
Downsampling takes only integers as parameters (rounds floats to the next lower integer)
Fixed
Bug in Analyze export of physical size of voxel size (22.09.05)
Crash when drawing below lower border (01.08.05)
When drawing points and drawing over border, points are drawn on the oppsite side (01.08.05)
Region growing wraps at image borders (31.07.05)
Tips & Hints
Improving Graph Cuts results
Segment your object by manually setting the seed points (brushs) in the Graph cuts dialog
Add the segmentation to the component image using value 9 (red color)
If the inital segmentation is not completely inside the object that should be segmented apply an erosion before adding to the component image
Apply a dilation on your initial segmentation
Add this to the component image using value 10 (green color)
Export the component image
Open again the Graph Cuts dialog and instead drawing manually seeds load the component image
Measuring diameters of long shaped segmented objects
Segment your object by satisfying mehtods
Generate the Distance Map and save it
Load the Distance Map as input image
Import your segmenation as output image
Extract the centerline with the Skeleton algorithm
Replace the voxel intensites of the output image with the values of the Distance Map
The values of centerline voxels are the distances to the object border (diameters)
Replacing background voxels by HU for Air
After resampling an CT image (e.g. for registration) the added voxels have intensity values of zero. To replace these values by Houndsfield units for air (-1024) do
the following steps
Resample or load a resampled image
Apply a region growing on the background voxels by setting upper and lower threshold to zero
Invert the segmentation
Choose "Replace Intensities" from the Segmentation menu, then choose "Input + HU Air"
