Convert3D documentation

Contents:

• Convert3D Documentation
  • What’s New?
  • About convert3d
  • Command autocompletion for Bash users
  • Coordinate Frames and NIFTI
  • Usage Examples
  • Multilabel Images
  • Commands: Image Input/Output and Information
    • -dicom-series-list: List image series in a DICOM directory
    • -dicom-series-read: Read a DICOM image series
    • -info: Display brief image information
    • -info-full: Display verbose image information
    • -mcs, -multicomponent-split: Enable splitting of multi-component images on read
    • -nomcs, -no-multicomponent-split: Disable splitting of multi-component images on read
    • -o: Output (write) last image on the stack to image file
    • -omc, -output-multicomponent: Output multiple images to single file
    • -oo: Output multiple images to multiple files
    • -oomc: Output multiple multi-component images to multiple files
  • Commands: Stack Manipulation and Flow Control
    • -accum, -endaccum: Accumulate operations over all images
    • -as: Assign image at the end of the stack to a variable
    • -clear: Clear the image stack
    • -foreach, -endfor: Loop commands over all images on the stack
    • -foreach-comp, -endfor: Loop commands over components of a multi-component image
    • -insert: Insert image anywhere in the stack
    • -pop: Remove last image from the stack
    • -popas: Remove last image from the stack and assign to variable
    • -push: Place variable at the end of the stack
    • -reorder: Rearrange images on the stack
    • -dup: Duplicate the last image on the stack
    • -pick: Select one or more images from the stack by index
  • Commands: Voxelwise Calculations
    • -abs: Voxelwise absolute value
    • -add: Voxelwise image addition
    • -atan2: Voxelwise angle from sine and cosine
    • -ceil: Round up image intensities
    • -clip: Clip image intensity to range
    • -composite: Composite one image onto another
    • -cos: Voxelwise cosine
    • -divide: Voxelwise image division
    • -exp: Voxelwise natural exponent
    • -erf: Standard error function
    • -floor: Round down image intensities
    • -log, -ln: Voxelwise natural logarithm
    • -log10: Voxelwise base 10 logarithm
    • -max: Voxel-wise maximum of two images
    • -min: Voxel-wise minimum of two images
    • -mean: Mean of all images on the stack
    • -multiply, -times: Multiply two images
    • -noise-gaussian, -noise: Apply additive Gaussian noise
    • -noise-poisson: Apply Poisson noise
    • -noise-salt-pepper: Apply salt and pepper noise
    • -noise-speckle: Apply Poisson noise
    • -otsu: Otsu’s thresholding
    • -reciprocal: Image voxelwise reciprocal
    • -replace: Replace intensities in image
    • -retain-labels: Retain labels in a label image
    • -rgb2hsv: Convert RGB image to HSV image
    • -rms: Voxelwise vector norm
    • -scale: Scale intensity by constant factor
    • -shift: Shift image intensity by constant
    • -sin: Sine
    • -sqrt: Take square root of image
    • -stretch: Stretch image intensities linearly
    • -thresh, -threshold: binary thresholding
    • -voxel-sum: Print sum of all voxel intensities
    • -voxel-integral: Print volume integral of all voxel intensities
    • -wsum, -weighted-sum: Weighed sum of images with constant weights
    • -wsv, -weighed-sum-voxelwise: Weighed sum of images with spatially varying weights
  • Commands: Image Header Manipulation
    • -copy-transform: Copy header information
    • -mbb, -match-bounding-box: Match bounding box of one image to another
    • -orient: Change image orientation
    • -origin: Set image origin
    • -origin-voxel: Assign image origin to a voxel
    • -origin-voxel-coord: Set coordinate of specified voxel
    • -set-sform: Set the transform to physical space
    • -spacing: Set voxel spacing
    • -swapdim: Reorder the coordinate axes of an image
  • Commands: Image Processing
    • -ad, -anisotropic-diffusion: Perona-Malik anisotropic diffusion filter
    • -biascorr: Automatic MRI bias field correction
    • -alm, -align-landmarks: Align images based on landmark matching
    • -binarize: Convert image to binary
    • -canny: Canny edge detector
    • -centroid: Report centroid of foreground voxels
    • -centroid-mark: Mark the centroid of foreground voxels
    • -color-map, -colormap: Convert scalar image to RGB using color map
    • -conv: Convolution
    • -comp, -connected-components: Compute connected components
    • -cmv, -coordinate-map-voxel: Generate voxel coordinate maps (voxel units)
    • -cmp, -coordinate-map-physical: Generate voxel coordinate maps (voxel units)
    • -create: Generate blank image
    • -dilate: Binary dilation
    • -erode: Binary erosion
    • -export-patches, -xp: Fixed size patch sampling from masked regions
    • -export-patches-aug, -xpa: data augmentation for deep learning
    • -fast-marching, -fm: Fast marching filter
    • -fm-dilate: Fast marching-based label dilation
    • -fft: Fast Fourier transform
    • -flip: Flip image around an axis
    • -glm: General linear model
    • -grad, -gradient: Image gradient
    • -hesseig, -hessian-eigenvalues: Compute eigenvalues of the Hessian matrix
    • -hessobj, -hessian-objectness: Hessian objectness filter
    • -holefill: Fill holes in binary image
    • -lstat, -label-statistics: Display segmentation volumes and intensity statistics
    • -lms, -landmarks-to-spheres: Generate image of spheres from landmark data
    • -laplacian, -laplace: Laplacian filter
    • -levelset: Level set segmentation
    • -mf, -mean-filter: Mean filter
    • -median, -median-filter: Median filter
    • -merge: Merge images from previous split command
    • -msq, -mean-square: Compute mean square difference metric
    • -mi, -mutual-info: Compute mutual informaiton metric
    • -mmi, -mattes-mutual-info: Compute mutual informaiton metric
    • -mci, -morphological-contour-interpolation: Interpolate labels
    • -ncc, -normalized-cross-correlation: Compute normalized cross-correlation image
    • -neck-trim: Trim away neck on brain MRI image
    • -nlm-denoise: Non-local Means Denoising
    • -nlm-upsample: Non-local Means Upsampling
    • -nmi, -normalized-mutual-info: Compute mutual informaiton metric
    • -ncor, -normalized-correlation: Compute normalized correlation metric
    • -nlw, -normalize-local-window: Standardize image intensity using local neighborhood
    • -oli, -overlay-label-image: Overlay segmentation image on grayscale image
    • -overlap: Compute relative overlap between binary images
    • -pad: Pad image with constant value
    • -pad-to: Pad image to desired size with constant value
    • -pad-to-multiple: Pad image to that the size is a multiple of some number
    • -pca: Principal components analysis of foreground voxels
    • -probe: Report image intensity at a voxel
    • -rank: Voxelwise ranking of intensity values
    • -rf-train: Train Random Forest classifier
    • -rf-apply: Apply Random Forest classifier
    • -region: Extract region from image
    • -resample: Resample image to new dimensions
    • -resample-iso: Resample image to (approximately) isotropic resolution
    • -resample-mm: Resample image to new resolution
    • -reslice-matrix: Resample image using affine transform
    • -reslice-itk: Resample image using affine transform
    • -reslice-identity: Resample image using identity transform
    • -sdt, -signed-distance-transform: Signed distance transform of a binary image
    • -sharpen: Sharpen edges in the image
    • -slice: Extract slices from an image
    • -slice-all: Extract slices from all images on the stack
    • -smooth: Gaussian smoothing
    • -smooth-fast: Fast approximate Gaussian smoothing
    • -smooth-multilabel: Apply Recursive Gaussian Smoothing to selected labels
    • -softmax: Compute softmax across all images on the stack
    • -split: Split multi-label image into binary images (all labels present)
    • -split-labels: Split multi-label image into binary images (specific labels)
    • -staple: STAPLE algorithm to combine segmentations
    • -steig, -structure-tensor-eigenvalues: Compute eigenvalues of the structure tensor
    • -test-image, -test-probe: Test condition
    • -tile: Tile and stack multiple images into one
    • -trim: Trim background region of image
    • -trim-to-size: Trim image to given size
    • -mv, -majority-vote: Majority vote among multilabel images on the stack
    • -vote: Vote among images on the stack
    • -vote-mrf: Vote with Markov Random Field regularlization
    • -voxreg, -voxelwise-regression: Regression between two images
    • -wrap: Wrap (rotate) image
  • Commands: Options and Parameters
    • -background: Specify background intensity
    • -compress, -no-compress: Enable/disable compression for some image files
    • -interpolation: Set interpolation mode
    • -noround, -round: Floating point rounding behavior
    • -pim, -percent-intensity-mode: Set behavior of % specifier
    • -rf-param-patch: Random Forest training patch size
    • -rf-param-usexyz: Random Forest coordinate features
    • -rf-param-treedepth: Random Forest tree depth
    • -rf-param-ntrees: Random Forest forest size
    • -spm, -nospm: SPM compatibility in Analyze output
    • -threads, -threads-all
    • -type: Specify pixel type for image output
    • -tolerance: overwrites the defaults ITK ImageToImageFilterCommon tolerances
    • -verbose: Enable verbose output of commands
  • Parameter Specifications
    • Vectors
    • Geometry
    • Intensity Values
  • File Format Notes
    • .hdr, .img, .img.gz
    • .cub
    • .df3
  • Support for Multicomponent Images
  • Commands with Variable Number of Parameters
  • How to Add a Command to C3D (For Software Developers)