It is the product of a decade-long collaboration between Paul Yushkevich, Ph. ITK-SNAP provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. Compared to other, larger open-source image analysis tools, ITK-SNAP design focuses specifically on the problem of image segmentation, and extraneous or unrelated features are kept to a minimum. The design also emphasizes interaction and ease of use, with the bulk of the development effort dedicated to the user interface. Version 3. Some of the core advantages of ITK-SNAP include: Linked cursor for seamless 3D navigation Manual segmentation in three orthogonal planes at once A modern graphical user interface based on Qt Support for many different 3D image formats, including NIfTI and DICOM Support for concurrent, linked viewing, and segmentation of multiple images Support for color, multi-channel, and time-variant images 3D cut-plane tool for fast post-processing of segmentation results Extensive tutorial and video documentation Compared to other, larger open-source image analysis tools, ITK-SNAP design focuses specifically on the problem of image segmentation, and extraneous or unrelated features are kept to a minimum.
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The user interface is correctly updated now. In addition, the BYU writer save geometric data as well. Two asserts were changed in exception throwing. These versions are now built nightly and will be distributed on SourceForge.
For this to work, we had to change to newer versions of the supporting libraries: ITK 3. The latter was necessary for 64 bit MacOS, which many users have requested.
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.
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. This addresses the request to get rid of the dotted line closing the polygon. This is useful for displaying statistical maps, where a certain fixed output range is desired. 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. 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. 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. 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. Also added a button to enable this feature; it is disabled by default. 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. 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. The layer inspector replaces the old "Image Information" and "Intensity Curve" windows. The color bar editor is only partially functional as of 1. 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. Use it with 'F3' to let the image occupy the whole screen. To use this functionality, users must run SNAP without "-g" or "-rgb" options: itksnap image. Users can enable automatic update checking.
Help and other HTML pages are now displayed in the operating system's own web browser, from itksnap. 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.
Of course this may not always work, but it should make a lot of frustrated users a little less frustrated. There is still room for improvement, of course. More memory is needed for mesh rendering, and a lot more for automatic segmentation.
When loading images in bit or bit formats, more memory may be required at the time of image IO. This memory is immediately deallocated though.
In all other modes, crosshair motion is accessible through MMB as well. This should speed up the reading of floating point images, for example. This makes interaction with the intensity curve and color map more real-time. 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.
It also affects the behavior of the Reorient Image dialog. Website Changes - The itksnap. Content can now be edited on the fly.
New in Version 1. 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. 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.
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. 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. For now, the user can only specify reorientations that are parallel to the anatomical axes. This will not affect users who simply view meshes in SNAP; however users who export meshes to other programs will be affected.
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.
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.
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