New end user features in GIMIAS 1 2 0

From user's Wiki!
Jump to: navigation, search

Open multiple data files from single folder

Added the possibility to open multiple data files from single folder and subfolders.

All files will be scanned from all subfolders. The files will be grouped using the file name without extensions and without the last digits. For example the file names demo-CT-pa15_OneChamber00.vtk and demo-CT-pa15_OneChamber01.vtk will be grouped into the data object called “demo-CT-pa15_OneChamber”.

Visualize Deformation Fields

Now is possible to visualize deformation fields as using a configurable Grid. The ITK transform will be used to transform each point of the grid.

Deformation field rendered over an image

Bounding Box selection

Added a new selection tool to select a bounding box on an image.

Bounding box

You can use the ctrl+left mouse button to move the markers.

3D Slicer plugin compatibility

Added compatibility with 3D Slicer framework.

3D Slicer

You can plug a 3D Slicer command line plugin into GIMIAS Framework. Added several 3D Slicer plugins:

  • Filtering.Arithmetic: Add Images, Cast Image, Mask Image, Substract Image
  • Registration: Fast Affine Registration, Fast NonRigid BSpline Registration, Fast Rigid Registration, Linear Registration
  • Filtering: CheckerBoard Filter, Histogram Matching, Image Label Combine, Otsu Threshold, Resample Scalar Volume, Resample Scalar/Vector/DWI Volume, Threshold Image, Voting Binary Hole Filling, Zero Crossing Based Edge Detection Filter
  • Converter: Create a DICOM Series, Orient Images
  • Filtering.Denoising: Curvature Anisotropic Denoising, Gaussian Blur, Gradient Anisotropic Diffusion, Median Filter
  • Filtering.Morphology: Grayscale Fill Hole, Grayscale Grind Peak
  • Surface Models: Label Map Smoothing, Merge Models, Polydata to LabelMap
  • Segmentation: Otsu Threshold Segmentation, Simple Region Growing

Working Area Configuration

Added the possibility to create your own working area at runtime. You can add as many views as you need and configure each view independently. All this configuration can be saved into an XML file that will be loaded by GIMIAS automatically next time.

Using the working area configuration widget you can create a new working area, rename it, save it into an XML file and delete an existing one.

Working area configuration

Data Selection Facility

Improved selection of data objects using a bulb light near each selectable input data in the input widget. When you have several data objects in the data tree, sometimes is difficult to know which rendered object matches the name in the data tree.

When you click on the input selector of a widget, you will see a bulb light near each selectable data.

Data selection

You can move the mouse pointer over the bulb light to show the desired object in the working area.

Data selection

Surface mesh closing methods


The aim of this tool is to close/fill the holes in a surface mesh. The user has the option to fill every hole in the mesh or to select the hole he wants to fill in (options "Close all" and "Choose Hole"). The output can be the surface mesh + the patches that have been computed or only the patches (option "Patch output only”). The user can finally choose between different methods of hole filling in order to find the one that fits better his needs (default method SmoothToCenter has been implemented in our lab by José Maria Pozo).

Close holes

How is it implemented in Gimias?

  • SINGLE_CENTER _POINT : A single point is added in the center and then triangles are created to cover the hole
  • RADIAL_TRIANGLES: A series of points are added in each radius from the center.
  • LINEAR_TO_CENTER_NONREDUCING_TRIANGLES : A series of linearly distributed concentric coronas with the same number of points.
  • LINEAR_TO_CENTER: A series of linearly distributed concentric coronas decreasing the number of points towards the center
  • SMOOTH_TO_CENTER: A series of roundedly distributed concentric coronas the number of points towards the center (default)."
  • SMOOTH_PATCH: Under development!
  • CLOSE_REFINER_FAIRER : based on the paper (ref) three steps are performed, closing the hole, then refining and fairing the patch

Volume Rendering Cropping Region Planes

The Volume Properties Widget now gives the possibility to crop the volume rendering of a 3d volume image according to user-defined cropping planes. When a volume image is loaded in Gimias and selected from the data tree, the volume properties widget will be automatically redrawn to include the Volume Rendering tab. This tab now includes three range-slider controls in the Cropping Planes section:

Clipping planes

By enabling the Enable VR checkbox, the volume rendering of the image will be displayed.

Now controlling each of the 3 sliders in the cropping planes area will permit to crop the volume rendering of the image in the corresponding direction (the sliders are ordered as x, y, z). For example, by regulating the y-slider like in the following figure, the result will be a cropped volume within the selected range in the y-direction (see below):

Clipping planes

Each cropping plane slider can be controlled just as the contrast and brightness bar: 1. By dragging one edge towards one direction, the range of the slider will be directly enlarged or restricted by keeping the symmetry respect to the actual slider center

2. By dragging the center of the slider, the center will be moved towards the dragging direction while the actual range will be kept unvaried

Integrative workflow example

As an example of the new features added into this Gimias version, an integrative workflow has been created, using ITK, MITK, VTK, GIMIAS and Netgen toolkits and using different data types to store the processing data.

Integrative workflow

In this workflow, 3 different plugin interfaces has been used: 3D Slicer, Raw DLL and GIMIAS.

For each step of the workflow, the required input data is different. For example, MITK filters need a mitk::Image as input. The input data is automatically converted to the required type.

These are the different steps of the workflow:

  • Gaussian Blur (ITK): Gaussian blur of an image
  • mitk::ImageToSurfaceFilter (MITK): Convert image to surface mesh
  • vtkWindowedSincPolyDataFilter (VTK): Smooth surface mesh
  • Ring Cut (GIMIAS): Cut a surface mesh using a ring
  • Volume Closing Surface (GIMIAS): Close all holes of a surface mesh
  • Netgen Optimization (NETGEN): Netgen surface mesh optimization

Gimias release for Mac OS X

First experimental release of GIMIAS for Mac OS X Snow Leopard (10.6.2).

Integrative workflow

How to launch Gimias on Mac Os X

Minimum Mac Os X version required: 10.6.2 (Snow Leopard)

N.B. Root user is disabled by default on Mac Os X. In the following it is assumed that you have enabled root account according to the procedure described for example in

  • Download and unzip the archive in one folder of your hard-drive (suppose /users/user_name/sw/gimias)
  • Open the terminal utility
  • Change to root user (with the su command) [or if you prefer you could execute the following commands with the sudo utility]
  • Go to the gimias folder (/users/user_name/sw/gimias)
  • If it is the first time you try to launch gimias in the current terminal session, type ./runGimias otherwise simply type ./gimias [the runGimias shell script first add the current directory to the DYLD_LIBRARY_PATH variable, in order to let the dynamic library loader (dyld) know where to find the required dylib]