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Size: 5.5K
R: Image Registration Using the 'NiftyReg' Library
...NEWS. Help Pages affine Create, test for and print affine matrices applyTransform Apply a precomputed transformation as.array.niftyreg Two and three dimensional image registration asAffine Create...
/CRAN/refmans/RNiftyReg/html/00Index.html
 cran-help  matching: image, image, registration and registration


Size: 5.3K
R: Transform image files using a registration or affine matrix
...Transform image files using a registration or affine matrix Description You should almost always call xform rather calling thanxformimage directly. Usage xformimage(reg, image, ...) ## S3 method...
/CRAN/refmans/nat/html/xformimage.html
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R: Reformat an image with a CMTK registration using the...
...an image with a CMTK registration using the reformatx tool Description Reformat an image with a CMTK registration using the reformatx tool Usage cmtk.reformatx( floating, registrations, output, target...
/CRAN/refmans/nat/html/cmtk.reformatx.html
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R: Construct templatebrain object for an image registration...
...brain in an image registration. Usually this will be a standard template brain used for many registrations. It will normally be much more convenient to use as.templatebrain methods to convert an image...
/CRAN/refmans/nat.templatebrains/html/templatebrain.html
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R: Two and three dimensional image registration
...registration Description The niftyreg function performs linear or nonlinear registration for two and three dimensional images. 4D images may also be registered volumewise to a 3D image, or 3D images...
/CRAN/refmans/RNiftyReg/html/niftyreg.html
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Size: 9.2K
R: Two and three dimensional linear image registration
...image registration Description The niftyreg.linear function performs linear registration for two and three dimensional images. 4D images may also be registered volumewise to a 3D image, or 3D images...
/CRAN/refmans/RNiftyReg/html/niftyreg.linear.html
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R: Two and three dimensional nonlinear image registration
...registration Description The niftyreg.nonlinear function performs nonlinear registration for two and three dimensional images. 4D images may also be registered volumewise to a 3D image, or 3D images...
/CRAN/refmans/RNiftyReg/html/niftyreg.nonlinear.html
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R: Register two images using 'ANTs'
...Register two images using 'ANTs' Description Register two images using 'ANTs' Usage ants_registration( fixed, moving, type_of_transform = "SyN", initial_transform = NULL, outprefix = tempfile(), mask...
/CRAN/refmans/rpyANTs/html/ants_registration.html
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R: Image to Image Co-Registration based on Mutual Information
...Image to Image Co-Registration based on Mutual Information Description Shifts an image to match a reference image. Matching is based on maximum mutual information. Usage coregisterImages( img, ref...
/CRAN/refmans/RStoolbox/html/coregisterImages.html
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R: Find optimum reparameterization between two images
...two images using the elastic framework Usage reparam_image(It, Im, gam, b, stepsize = 1e-05, itermax = 1000, lmark = FALSE) Arguments It template image matrix Im test image matrix gam initial warping...
/CRAN/refmans/fdasrvf/html/reparam_image.html
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R: Pairwise align two images This function aligns to images...
...align two images This function aligns to images using the q-map framework Description Pairwise align two images This function aligns to images using the q-map framework Usage pair_align_image( I1, I2...
/CRAN/refmans/fdasrvf/html/pair_align_image.html
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R: Find sequence of one or more bridging registrations
...of one or more bridging registrations Description This function is primarily intended for developer use (it is used inside xform_brain) but may be useful for end users. Usage bridging_sequence( sample...
/CRAN/refmans/nat.templatebrains/html/bridging_sequence.html
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R: Default UI styles for the Sign In & Registration pages
...Registration pages Description Default styling for the sign in & registration pages. Update the sign_in_ui_default() arguments with your brand and colors to quickly style the sign in & registration...
/CRAN/refmans/polished/html/sign_in_ui_default.html
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R: Register using FNIRT, but doing Affine Registration as well
...doing Affine Registration as well Description This function calls fnirt to register infile to reffile and either saves the image or returns an object of class nifti, but does the affine registration...
/CRAN/refmans/fslr/html/fnirt_with_affine.html
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R: Transform 3D points using a registration, affine matrix or...
...Transform 3D points using a registration, affine matrix or function Description You should almost always call xform rather calling thanxformpoints directly. Usage xformpoints(reg, points, ...) ## S3...
/CRAN/refmans/nat/html/xformpoints.html
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R: Make in-memory CMTK registration list from affine matrix or...
...registration list from affine matrix or CMTK parameters Usage cmtkreglist(x, centre = c(0, 0, 0), reference = "dummy", floating = "dummy") Arguments x 5x3 matrix of CMTK registration parameters OR 4x4...
/CRAN/refmans/nat/html/cmtkreglist.html
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R: Make or query connected graph of bridging registrations
...known template brains (vertices) and the bridging registrations connecting them (edges). shortest_bridging_seq finds the shortest bridging sequence on a graph of all available bridging registrations...
/CRAN/refmans/nat.templatebrains/html/shortest_bridging_seq.html
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R: Aligns images using 'niftyreg' utilities for automated image...
...Aligns images using niftyreg utilities for automated image registration.. Description Aligns images using niftyreg utilities for automated image registration.. Usage alignReg( sampleList, target...
/CRAN/refmans/patternize/html/alignReg.html
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R: Aligns images using 'niftyreg' utilities for automated image...
...images using niftyreg utilities for automated image registration and extracts colors using k-means clustering. Description Aligns images using niftyreg utilities for automated image registration...
/CRAN/refmans/patternize/html/patRegK.html
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R: Aligns images using 'niftyreg' utilities for automated image...
...images using niftyreg utilities for automated image registration and extracts colors using k-means clustering. Description Aligns images using niftyreg utilities for automated image registration...
/CRAN/refmans/patternize/html/patRegK_HSV.html
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R: Aligns images using 'niftyreg' utilities for automated image...
...automated image registration and extracts colors using a predefined RGB values and cutoff value. Description Aligns images using niftyreg utilities for automated image registration and extracts colors...
/CRAN/refmans/patternize/html/patRegRGB.html
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R: Aligns images using 'niftyreg' utilities for automated image...
...automated image registration and extracts colors using a predefined HSV values and cutoff value. Description Aligns images using niftyreg utilities for automated image registration and extracts colors...
/CRAN/refmans/patternize/html/patRegHSV.html
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R: Aligns images using 'niftyreg' utilities for automated image...
...Aligns images using niftyreg utilities for automated image registration and extracts color pattern using watershed segmentation. This function works interactively by allowing to pick a starting pixel...
/CRAN/refmans/patternize/html/patRegW.html
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R: Call Image Colorization API
...images to be colorized. key DeepAI API key. pane defines in which pane the image is displayed: plot, view or none. Details With the default API key a few queries are possible. After registration on...
/CRAN/refmans/colorizer/html/colorize.html
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R: Example Image Data set
...Example Image Data set Description Contains two simulated images for registration. Usage im Format im A list with two components: I1: A numeric matrix of shape 64 \times 64 storing the 1st image; I2...
/CRAN/refmans/fdasrvf/html/im.html
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R: Similarity measures between images
...by the registration algorithms. Usage similarity(source, target, targetMask = NULL, interpolation = 3L, threads = getOption("RNiftyReg.threads")) Arguments source The source image, in any acceptable ...
/CRAN/refmans/RNiftyReg/html/similarity.html
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R: Degradation of an image
...z a cimgobject containing the high resolution image L numeric indicating the overall scale change. This parameter will be override by L1 or L2 s numeric p by 2 matrix containing the registration...
/CRAN/refmans/redR/html/degrade.html
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R: Transform an image
...image Description Transform an image Usage transform(im, s) Arguments im cimg object s numeric 1 by 3 vector containing the registration parameters Value shifted cimg object Examples shift(cameraman...
/CRAN/refmans/redR/html/transform.html
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R: NeuroAnatomy Toolbox for Analysis of 3D Image Data
...Pages A B C D E F G H I K M N O P R S T U V W X misc nat-package Analyse 3D biological image data especially neurons -- A -- affmat2cmtkparams Decompose homogeneous affine matrix to CMTK registration...
/CRAN/refmans/nat/html/00Index.html
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R: NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains
...folders containing registrations for nat.templatebrains allreg_dataframe Make data.frame with details of all registrations all_templatebrains Find all template brains or those matching a given image...
/CRAN/refmans/nat.templatebrains/html/00Index.html
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R: patternize - An R package for quantifying color pattern...
...images. Patternize is an R package that quantifies variation in color patterns as obtained from image data. Patternize defines homology between pattern positions across specimens either through fixed...
/CRAN/refmans/patternize/html/patternize.html
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R: Quantification of Color Pattern Variation
...images using landmarks alignReg Aligns images using 'niftyreg' utilities for automated image registration.. colorChecker Calibrate images using ColorChecker. colorChecker_customGray Calibrate images...
/CRAN/refmans/patternize/html/00Index.html
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R: Analyse 3D biological image data especially neurons
...Analyse 3D biological image data especially neurons Description nat provides tools to read, analyse, plot, transform and convert neuroanatomical data, especially representations of neurons. Neuron...
/CRAN/refmans/nat/html/nat-package.html
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R: Transform 3D object between template brains
...Transform 3D object between template brains Usage xform_brain( x, sample = regtemplate(x), reference, via = NULL, imagedata = is.character(x), checkboth = NULL, target = NULL, Verbose = interactive(), ...
/CRAN/refmans/nat.templatebrains/html/xform_brain.html
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R: Mirror 3D object about a given axis, optionally using a...
...a warping registration Description mirroring with a warping registration can be used to account e.g. for the asymmetry between brain hemispheres. mirror.character handles images on disk Usage mirror(x...
/CRAN/refmans/nat/html/mirror.html
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R: Reverse-Phase Protein Array Super Position and Concentration Evaluation
...Pages C D F G H I L N P Q R S T W RPPASPACE-package Reverse phase protein lysate array analysis -- C -- CobsFitClass-class Class "CobsFitClass" coef-method Class "RPPAFit" coef-method Class "FitClass"...
/CRAN/refmans/RPPASPACE/html/00Index.html
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R: 'rsat'
...("rsat2_download", package = "rsat")) Customize, and (run vignette("rsat3_customize", package = "rsat")) Process (run vignette("rsat4_process", package = "rsat")) satellite images from Landsat, MODIS...
/CRAN/refmans/rsat/html/rsat.html
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R: Preprocess MRI scans for multiple patients
...imhomogeneity correction 'N4', linear coregistration of T2-weighted and/or FLAIR to the T1-weighted, registration of all available modalities to the MNI152 template with an isotropic voxel size of 1mm...
/CRAN/refmans/neuronorm/html/preprocess_patients.html
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R: REgularization by Denoising (RED)
...images via FFT lenna Photograph of Lenna MAE Error measurements of images MSE Error measurements of images PSNR Error measurements of images RED RED: Regularization by Denoising register Registration...
/CRAN/refmans/redR/html/00Index.html
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R: Motion correction
...x input image, usually 'fMRI' series fixed fixed image to register all timepoints to type_of_transform see ants_registration mask mask for image fdOffset offset value to use in frame-wise displacement...
/CRAN/refmans/rpyANTs/html/ants_motion_correction.html
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R: Preprocess T1-weighted MRI scan for one patient
...preprocesses a raw T1-w MRI scan and generates a segmentation MRI scan using the FAST algorithm. The preprocesising steps comprises imhomogeneity correction 'N4', registration to the MNI152 template...
/CRAN/refmans/neuronorm/html/preprocess_modality_t1.html
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R: Intersects a RasterStack with an outline. Everything outside...
...outline, refShape, landList = NULL, adjustCoords = FALSE, cartoonID = NULL, IDlist = NULL, crop = c(0, 0, 0, 0), flipRaster = NULL, flipOutline = NULL, imageList = NULL, maskColor = 0, inverse...
/CRAN/refmans/patternize/html/maskOutline.html
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R: Evaluate NOPS Exams
...NOPS exams produced with exams2nops, and scanned by nops_scan. Usage nops_eval(register = dir(pattern = "\\.csv$"), solutions = dir(pattern = "\\.rds$"), scans = dir(pattern = "^nops_scan_[[:digit...
/CRAN/refmans/exams/html/nops_eval.html
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R: Preprocess group of MRI scan for one patient
...segmentation MRI scan using the FAST algorithm. The preprocesising steps comprises imhomogeneity correction 'N4', coregistration of other sequences to the T1-weighted scan, non-linear registration to...
/CRAN/refmans/neuronorm/html/preprocess_modalities.html
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Size: 3.3K
R: MRI Defacer
..."-f 0.5", search_radius = 90, opts = NULL, template_brain = NULL, template_brain_weight = NULL, template_biometric_mask = NULL, verbose = TRUE ) Arguments file input file image to remove face/ears ...
/CRAN/refmans/fslr/html/mridefacer.html
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Size: 8.7K
R: Transform the 3D location of objects such as neurons
...designed to operate on a variety of data types, especially objects encapsulating neurons. xform depends on two specialised downstream functions xformpoints and xformimage. These are user visible any...
/CRAN/refmans/nat/html/xform.html
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R: Read Scanned NOPS Exams
...n = NULL, density = 300, size = 0.03, threshold = c(0.04, 0.42), trim = 0.3, minrot = 0.002, string = FALSE) Arguments images character. Names of the PDF/PNG images containing the scanned exams. By...
/CRAN/refmans/exams/html/nops_scan.html
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R: Run FIRST All
...the input image (T1-weighted) oprefix specifies the output image basename (extensions will be added to this) brain_extracted specifies that the input image has been brain extracted structures...
/CRAN/refmans/fslr/html/run_first_all.html
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Size: 5.2K
R: Plot color pattern prediction for specified PCA values
...PCA values Usage createPhenotype( PCAdata, PCApredict, IDlist, rasterList, colpalette = NULL, plotCartoon = FALSE, refShape = NULL, outline = NULL, lines = NULL, landList = NULL, adjustCoords = FALSE...
/CRAN/refmans/patternize/html/createPhenotype.html
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R: Read CMTK TypedStream file to a list in memory
...registrations and landmarks. Usage read.cmtk(con, CheckLabel = TRUE) Arguments con Path to (optionally gzipped) file or (open) connection. CheckLabel Check, fix and warn for invalid or duplicate...
/CRAN/refmans/nat/html/read.cmtk.html
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R: Remote Sensing Data Analysis
...Terrain coregisterImages Image to Image Co-Registration based on Mutual Information decodeQA Decode QA flags to bit-words encodeQA Encode QA Conditions to Integers estimateHaze Estimate Image Haze...
/CRAN/refmans/RStoolbox/html/00Index.html
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R: This fucntion calculates the area in which the color pattern...
...pattern is expressed in each sample as the relative proportion using the provided outline of the considered trait or structure. Usage patArea( rList, IDlist, refShape, type, outline = NULL, landList...
/CRAN/refmans/patternize/html/patArea.html
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R: Return path to directory containing CMTK binaries
...image registration toolkit supported by nat. An external CMTK installation is required in order to apply CMTK registrations. This function attempts to locate the full path to the CMTK executable files...
/CRAN/refmans/nat/html/cmtk.bindir.html
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R: Plots the color pattern heatmaps from 'sumRaster' output.
...color pattern heatmaps from sumRaster output. Description Plots the color pattern heatmaps from sumRaster output. Usage plotHeat( summedRaster, IDlist, colpalette = NULL, plotCartoon = FALSE, refShape...
/CRAN/refmans/patternize/html/plotHeat.html
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R: Extract forward and reverse transformations
...These functions extract forward and reverse transformations in a form compatible with applyTransform and other functions. They are (S3) generic, but only methods for "niftyreg" objects currently exist.
/CRAN/refmans/RNiftyReg/html/forward.html
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R: Class "dwi"
...Weighted Imaging (DWI) data and, within the Diffusion Tensor Model (DTI), diffusion tenors and its indices. Objects from the Class "dwi" is only a superclass, no instances should be created. However...
/CRAN/refmans/dti/html/dti-class.html
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R: This function transforms the individual color pattern rasters...
...function transforms the individual color pattern rasters as obtained by the main patternize functions to a dataframe of 0 and 1 values that can be used for constrained Redundancy Analysis (RDA) (rda).
/CRAN/refmans/patternize/html/patRDA.html
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R: This function transforms the individual color pattern rasters...
...(prcomp). This function also allows to plot the analysis including a visualization of the shape changes along the axis. Pixel values are predicted by multiplying the rotation matrix (eigenvectors)...
/CRAN/refmans/patternize/html/patPCA.html
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R: 20 traced Drosophila neurons from Chiang et al 2011
...shared their raw data. Automated tracing of neuron skeletons was carried out by Lee et al [2]. Image registration and further processing was carried out by Greg Jefferis, Marta Costa and James Manton...
/CRAN/refmans/nat.nblast/html/fctraces20.html
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R: List of 3 matrices containing 3D points from Drosophila...
...tw. Image registration and further processing was carried out by Greg Jefferis. References [1] Chiang A.S., Lin C.Y., Chuang C.C., Chang H.M., Hsieh C.H., Yeh C.W., Shih C.T., Wu J.J., Wang G.T., Chen...
/CRAN/refmans/nabor/html/kcpoints.html
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R: Register/deregister the parallel backend
...framework depends on the container image. If the container uses the foreach framework, there is no need to define deregisterParallelBackend as its default method will deregister the foreach backend.
/CRAN/refmans/DockerParallel/html/containerParallelBackend.html
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R: Normalizes multiplexed data
...image input according to the method specified Usage mx_normalize( mx_data, transform = "None", method = "None", method_override = NULL, method_override_name = NULL, ... ) Arguments mx_data mx_dataset...
/CRAN/refmans/mxnorm/html/mx_normalize.html
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R: Cloud Shadow Masking for Flat Terrain
...select a few corresponding cloud/cloudShadow pixels which will be used to estimate coordinates for a linear cloudmask shift. Usage cloudShadowMask( img, cm, nc = 5, shiftEstimate = NULL, preciseShift...
/CRAN/refmans/RStoolbox/html/cloudShadowMask.html
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R: MAGIC Gamma Telescope
...registration of high energy gamma particles in a Major Atmospheric Gamma-Ray Imaging Cherenkov (MAGIC) Gamma Telescope. The task is to distinguish gamma rays (signal) from hadronic showers (background).
/CRAN/refmans/evtree/html/MAGICGammaTelescope.html
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R: Optical Flow
optflow {SpatialVx} R Documentation Optical Flow Description Estimate the optical flow from one gridded field (image) to another. Usage optflow(initial, final, grads.diff = 1, mean.field = NULL...
/CRAN/refmans/SpatialVx/html/optflow.html
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R: Bookstein's schizophrenia data
...fourteen cases were diagnosed with schizophrenia. The landmarks were taken in the near midline from MR images of the brain: (1) splenium, posteriormost point on corpus callosum; (2) genu, anteriormost...
/CRAN/refmans/shapes/html/schizophrenia.dat.html
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R: List of 20 Kenyon Cells from Chiang et al 2011 converted to...
...20 skeletonized Drosophila Kenyon cells as dotprops objects. Original data is due to Chiang et al. 2011, who have generously shared their raw data doi:10.1016/j.cub.2010.11.056. Image registration...
/CRAN/refmans/nat/html/kcs20.html
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Size: 2.7K
R: Bookstein's schizophrenia data
...14 individuals are controls. The last fourteen cases were diagnosed with schizophrenia. The landmarks were taken in the near midline from MR images of the brain: (1) splenium, posteriormost point on...
/CRAN/refmans/shapes/html/schizophrenia.html
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Size: 39.6K
R: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')
...applytopup - calling FSL applytopup apply_topup applytopup - calling FSL applytopup aux.file-method Extract Image aux.file attribute aux.file-methods Extract Image aux.file attribute avscale Scale...
/CRAN/refmans/fslr/html/00Index.html
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R: Generation of Written Exams for Automatic Evaluation
..."en", title = "Exam", course = "", institution = "R University", logo = "Rlogo.png", date = Sys.Date(), replacement = FALSE, intro = NULL, blank = NULL, duplex = TRUE, pages = NULL, usepackage...
/CRAN/refmans/exams/html/exams2nops.html
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Size: 8.3K
R: Get a spatial basemap
...set_defaults can be used to define basemap preferences once for the running session. Usage basemap( ext = NULL, map_service = NULL, map_type = NULL, map_res = NULL, map_token = NULL, map_dir = NULL...
/CRAN/refmans/basemaps/html/basemap.html
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R: Calculations and Visualisations Related to Geometric Morphometrics
...related to Geometric Morphometrics and shape analysis -- A -- align2procSym align new data to an existing Procrustes registration angle.calc calculate angle between two vectors angleTest Test whether ...
/CRAN/refmans/Morpho/html/00Index.html
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Size: 29.2K
R: Interface to the 'Azure Machine Learning' 'SDK'
...an ACI web service aks_webservice_deployment_config Create a deployment config for deploying an AKS web service attach_aks_compute Attach an existing AKS cluster to a workspace azureml azureml ...
/CRAN/refmans/azuremlsdk/html/00Index.html
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R: Tools for Package Development
Help Pages A B C D E F G H L M N P Q R S T U V W X misc tools-package Tools for Package Development -- A -- activeConcordance Concordance between source and target lines add_datalist Add a 'datalist'...
/R/refmans/tools/html/00Index.html
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R: Optical Flow Verification
...Perform verification using optical flow as described in Marzban and Sandgathe (2010). Usage OF(x, ...) ## Default S3 method: OF(x, ..., xhat, W = 5, grads.diff = 1, center = TRUE, cutoffpar = 4...
/CRAN/refmans/SpatialVx/html/OF.html
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Size: 10.2K
R: Coordinates for data from brain atlases
...spatial coordinates for: the original AAL atlases, the newer AAL2 atlases, Freesurfer atlases, Brainsuite, Craddock200, Dosenbach160, Harvard-Oxford, and LONI probabilistic brain atlas. In addition...
/CRAN/refmans/brainGraph/html/brain_atlases.html
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R: Linear Model for fMRI data
...fmri.lm(ds, z, mask = NULL, actype = c("smooth", "noac", "ac", "accalc"), contrast = c(1), verbose = FALSE) Arguments ds Data object of class "fmridata" z Design matrix specifying the expected BOLD...
/CRAN/refmans/fmri/html/fmri.lm.html
 cran-help  matching: image and registration


Size: 21.8K
R: Spatial Forecast Verification
...Methods: 1a. Neighborhood Methods: Neighborhood methods generally apply a convolution kernel smoother to one or both of the fields in the verificaiton set, and then apply the traditional scores. Most...
/CRAN/refmans/SpatialVx/html/SpatialVx-package.html
 cran-help  matching: image and registration


Size: 8.9K
R: Varved sediment data from lake Kassjön
...covariates. The varved sediment of lake Kassjön covers approximately 6400 years and is believed to be historical records of weather and climate. The varves (years) are clustered into similar groups...
/CRAN/refmans/fdaMocca/html/varve.html
 cran-help  matching: image and registration


Size: 11.4K
R: Creates a launch configuration
...LaunchConfigurationName, ImageId = NULL, KeyName = NULL, SecurityGroups = NULL, ClassicLinkVPCId = NULL, ClassicLinkVPCSecurityGroups = NULL, UserData = NULL, InstanceId = NULL, InstanceType = NULL...
/CRAN/refmans/paws.management/html/autoscaling_create_launch_configuration.html
 cran-help  matching: image and registration


Size: 55.0K
R: MR Spectroscopy Analysis Tools
...NEWS. Help Pages A B C D E F G H I K L M N O P Q R S T V W Z spant-package spant: spectroscopy analysis tools. -- A -- abfit_opts Return a list of options for an ABfit analysis. abfit_opts_v1_9_0...
/CRAN/refmans/spant/html/00Index.html
 cran-help  matching: image and registration


Size: 15.6K
R: ICU datasets
...Physiology (LCP) at MIT hosts several large-scale databases of hospital intensive care units (ICUs), two of which can be either downloaded in full (MIMIC-III and eICU ) or as demo subsets (MIMIC-III...
/CRAN/refmans/ricu/html/data_env.html
 cran-help  matching: image and registration




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