Rhino3DMedical documentation

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Rhino3DMedical documentation

Version 1.0.4.0 Rhino Commands RMEraser

• Tool to remove mask regions from current Manual Segmentation mask RMExtractLargestRegion

• Given a mesh, extract the single largest connected surface RMFillMeshHoles

• Given a mesh, try to fill the holes automatically and create a closed mesh RMGetRegionGrowingSeedPoint

• Select the seed point for the Region Growing Algorithm RMImageAnalysis

• Open the Image Analysis window • Functionalities of this window

o Explore the image in the sagittal, coronal or axial plane o Adjust the contrast

o Adjust the coloring

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2 of 9 RMImageFilters

• Open the Image Filters window • Available Filters

o Gaussian Smoothing

▪ reduces noise by averaging over a window o Gradient Magnitude

▪ detects edges in the image o Dilation

▪ increases light areas o Erosion

▪ increases dark areas o Opening

▪ removes small dark areas o Closing

▪ removes small light areas o Median

▪ reduces noise by taking the median over a window • The diameter of all filters can be changed

RMLicense

• Check the status of your license, deactivate the current or activate a new one RMMaskFromClosedCurve

• Add/Subtract/Intersect the content of a closed curve with the manual segmentation mask RMMaskFromBrep

• Add/Subtract/Intersect the bounding box of a brep with the manual segmentation mask RMMeshRepair

• Open the Mesh Repair window • Available tools

o Extract largest region

▪ Extracts the largest connected mesh o Fill mesh holes

▪ Attempts to fill all openings and produce a closed mesh o Smoothen mesh

▪ Reduces jagged parts in the mesh o Remesh

▪ Reduces the number of triangles by a set percentage RMOpenImage

• Open a new image in any supported format • The currently supported formats are

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3 of 9 o MetaImage (*.mhd / *.mha)

o NIFTI (*.nii / *.nii.gz) o NRRD (*.nrrd) o TIFF (*.tif / *.tiff)

o DICOM (single image, single series, multiple series) • To read a DICOM, select any file from the series

• When reading DICOM series, its related metadata is printed in Rhino Command Prompt RMRefocusImage

• Center the views in Rhino on the current image RMRemesh

• Given a mesh, reduce the number of faces by a given percentage RMResizeImage

• Test command

• Given an input factor, the active image will be downscaled as many times as the input factor RMSegmentation

• Open the Segmentation window • Available segmentations:

o From a threshold

▪ Uses the threshold range defined in the Image Analysis window ▪ Includes an option to automatically produce closed meshes ▪ May produce multiple disconnected meshes

o From region growing:

▪ Uses the threshold range defined in the Image Analysis window ▪ Will only produce a single mesh, containing the selected point ▪ Includes an option to automatically produce closed meshes o From manual segmentation

▪ Allows creating a manually defined mask

▪ Create mask from threshold defined in Image Analysis

▪ Clip mask with a bounding box: ‘Create’ generates the bounding box, ‘Apply' applies its clipping onto the mask, ‘Cancel’ removes the bounding box

▪ Paint mask: ‘Paint' lets the user select a slice and directly paint on top of it (use SHIFT to instead erase mask, ALT to change the picker size), ‘Delete on slice’ removes the mask from a single slice , ‘Delete all’ removes the whole mask, ‘Size’ changes the picker size, ‘Shape’ changes the picker shape (between circle and square)

▪ Fill between slices

▪ Option to show/hide mask and change its color ▪ Create surface from mask

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4 of 9 RMSelectImage

• Select an image stack to be the active one and apply our methods RMSmoothenMesh

• Given a mesh, apply the Laplacian mesh smoothing filter to reduce sharp edges RMSurfaceFromMask

• Create mesh from the manual segmentation mask • Option to produce a closed mesh

RMSurfaceFromRegionGrowing

• Creates the surface according to the current thresholds and a selected point o displays the value of the pixel under the cursor in real time

• Option to produce a closed mesh

• Option to grow over mask instead of thresholds

• Can only be applied if the Rhino3DMedical dialog is active RMSurfaceFromThreshold

• Creates the surface according to the current thresholds • Option to produce a closed mesh

• Option to extract largest region

• Can only be applied if the Rhino3DMedical dialog is active RMSwitchLinearInterpolation

• Switch image pixel representation between nearest neighbors and linear interpolation (by default it is nearest neighbors)

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5 of 9 Grasshopper Components

Extract Slice

• Get a single slice

o The slice is returned as a mesh with vertex colors

• IN Image (I) [custom object no default]

• IN Plane (P) [integer default=0]

o 0 = XY, 1 = XZ, 2 = YZ

• IN Number (N) [number default=0]

o slice number to be displayed

o clamped to the extents if it exceeds them

• OUT Slice (S) [mesh]

o The resulting mesh with vertex colors Get Bounding Box

• Get the bounding box of an image

• OUT BBox (B) [box]

Get Extents

• Get the extents of an image in the X, Y and Z direction

o The extents are the valid indices in any direction, useful for the ExtractSlice component

• OUT XExtents (X) [interval]

• OUT YExtents (Y) [interval]

• OUT ZExtents (Z) [interval]

o The size in the X, Y, and Z dimension Get Range

• Get the intensity range of an image

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6 of 9 ImageFilter Close

• Applies closing operation to a 3D volume

o Removes small holes (dark areas) from the image o Equivalent to dilation followed by erosion

• IN Size (S) [integer default=5]

o Size of the dilation and erosion kernel

• OUT Image (I) [custom object]

ImageFilter Dilate

• Applies dilation operation to a 3D volume o Enhances objects (bright areas)

o Size of the dilation kernel

ImageFilter Erode

• Applies erosion operation to a 3D volume o Enhances holes (dark areas)

o Size of the erosion kernel

ImageFilter Gradient

• Computes the magnitude of the gradient of the image

ImageFilter Median

• Compute the local median for each pixel o Useful for noise removal

o Size of the median kernel

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7 of 9 ImageFilter Open

• Applies opening operation to a 3D volume

o Removes small objects (bright areas) from the image o Equivalent to erosion followed by dilation

o Size of the dilation and erosion kernel

ImageFilter Smooth

• Applies gaussian smoothing to a 3D volume

• IN Size (S) [number default=3.0]

o Size of the gaussian blur kernel

License

• Validate / disable / modify the installed license

• IN ShowWindow (S) [boolean default=false]

o If true display the wizard for modifying the state of your license or activating another

• OUT IsValid (I) [boolean]

o Whether license is valid MeshFilter Fill Holes

• Creates a closed mesh by filling any openings in a mesh

o If the input mesh is closed this component doesn’t modify it

• IN Mesh (M) [mesh no default]

o Input mesh, open or closed

• OUT Mesh (M) [mesh]

o Closed output mesh

Read File

• Read a MetaImage, NIFTI, DICOM, NRRD, TIFF file

o To read a DICOM series, input the path of any file in the series

• IN Path (P) [text no default]

o The path to the file

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8 of 9 Surface from Region Growing

• Create the surfaces from a given 2 thresholds and a point

• IN LowerThreshold (LT) [number default=0]

• IN UpperThreshold (UT) [number default=1000]

o Lower and upper threshold may also be flipped, which one has the smaller value is not important

• IN Point (P) [3D Point default=0,0,0]

o The point from which to grow the region

• IN Close (C) [boolean default=false]

o Whether to return a closed mesh • IN Smooth (S) [boolean default=true]

o Whether to produce a smooth output

o If this is set to false, the result may have jagged bumps in it

• OUT Mesh (M) [mesh]

Surface from Threshold

• Create a surface from a given list of thresholds

o The 3D image object

• IN Threshold (T) [number list default=1000]

o Thresholds for extracting the mesh

o If there are 2 thresholds a single closed surface can be created

• IN Close (C) [boolean default=false]

o Whether to return a closed mesh or a surface • IN Smooth (S) [boolean default=true]

o Whether to produce a smooth output

o If this is set to false, the result may have jagged bumps in it

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9 of 9 Download Direct http://download.mirrakoi.com/download?file=Rhino3DMedicalInstaller.exe Website https://rhino3dmedical.mirrakoi.com/ Update