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-1- Roundup of Useful AFNI Programs and Plugins Dataset Creation and Conversion to3dRead image files, write AFNI format datasets 3dAFNIto3DConvert AFNI.

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Presentation on theme: "-1- Roundup of Useful AFNI Programs and Plugins Dataset Creation and Conversion to3dRead image files, write AFNI format datasets 3dAFNIto3DConvert AFNI."— Presentation transcript:

1 -1- Roundup of Useful AFNI Programs and Plugins Dataset Creation and Conversion to3dRead image files, write AFNI format datasets 3dAFNIto3DConvert AFNI format dataset to.3D format (ASCII lists) 3dAFNItoANALYZEConvert AFNI format dataset to ANALYZE format 3dAFNItoMINCConvert AFNI format dataset to MINC format 3dANALYZEtoAFNIConvert ANALYZE format dataset to AFNI format 3dMINCtoAFNIConvert MINC format dataset to AFNI format 3dThreetoRGBConvert 3 scalar datasets to 1 RGB AFNI format dataset Auxiliary Programs for Dataset Creation from Images IfileRead GE realtime EPI files and runs to3d ImonRead GE realtime EPI files as they are created DimonRead DICOM files as they are created rtfeedmeDissect one dataset, sends images to AFNi reatime plugin plugin: RT OptionsControl options for AFNI realtime image input from3dWrite dataset slices into image files abutCreate zero-filled slices to put into dataset gaps Quality Checks for 3D+time Datasets 3dToutcountCheck voxel time series for quality (temporal outliers) 3dTqualCheck dataset sub-bricks for quality (spatial outliers)

2 -2- 3D+time Pre-Processing Programs 3DTshiftShift slices to a common time origin (temporal interpolation) 3dDespikeRemove spikes from voxel time series 3dDetrendRemove trends from voxel time series 3DFourierFFT-based lowpass and highpass filtering 3dTsmoothSmooth time series in the time domain 3D+time Analysis Programs 3dDeconvolveMultiple linear regression and deconvolution plugin: DeconvolutionInteractive deconvolution 3dfimSingle regression linear analysis 3dfim+Extended version of 3dfim 3ddelaySingle regressor linear analysis with time shifting 3dNLfimNonlinear regression plugin: Nlfit & NlerrInteractive nonlinear regression 3dTcorrelateCorrelate two input datasets, voxel-by-voxel 3dAutoTcorrelateCorrelate each voxel with every other voxel 3dpcPrincipal component analysis Model 1D Time Series Generators sqwaveGenerate a square wave (a very old program) waverGenerate hemodynamic responses to stimulus time series

3 -3- Dataset Histogram Programs 3dAnhistCreate and plot histogram of dataset, print peaks 3dhistogCreate histogram of dataset to a file plugin: HistogramInteractively graphs histogram of a dataset (or ROI) plugin: ScatterPlotInteractively graphs 1 sub-brick vs. another (or ROI) 3dClipLevelFind value to threshold off outside-the-brain voxels 3dUniformizeCorrect T1-weighted dataset for non-uniform histogram 3dIntracranialStrip off outside-the-brain voxels 3dSkullStripEnhanced skull stripping Group Dataset Statistical Analysis Programs 3dttestPaired and unpaired t-tests 3dANOVA1-way ANOVA (fixed effects) 3dANOVA22-way ANOVA (fixed, random, mixed effects) 3dANOVA33-way ANOVA (fixed, random, mixed effects) GroupAnan-way (1-5) ANOVA (MatLab script) 3dFriedmanNonparametric Friedman test 3dKruskalWallisNonparametric Kruskal-Wallis test 3dWilcoxonNonparametric Wilcoxon test 3dMannWhitneyNonparametric 3dMannWhitney test 3dRegAnaVoxel-wise linear regression analyses 3dFDRFalse Discovery Rate analysis

4 -4- Programs for Manipulating Information in the Dataset Header 3dinfoPrint out information from the header 3dAttributePrint out a single header attribute 3dnewidAssign a new ID code to a dataset 3drefitLets you change attributes in a dataset header 3dNotesLets you put text notes into a dataset header plugin : Dataset NOTESInteractive header notes editor nifti_toolDisplays, modifies, copies nifti structures in datasets Programs for Changing Dataset Spatial Structure 3daxializeRewrite dataset with slices in different direction 3dresampleRewrite dataset in new orientation, with new voxel size 3dLRflipFlip dataset Left  Right Programs for Assembling Sub-bricks into 4D Datasets 3dTcatAssemble a 3D+time dataset from multiple input sub-bricks 3dbucketAssemble a bucket dataset from multiple input sub-bricks Programs for Changing Slice Structure 3dZcatGlue multiple sub-bricks together along the z-axis 3dZcutupCut slices out of a dataset to make a ‘thinner’ dataset 3dZeropadAdd zero slices around the edges of a dataset 3dZregridInterpolate a dataset to a different slice thickness

5 -5- Spatial Transformations of Dataset Geometry 3drotateRigid body rotation of dataset in 3D 3dWarpNon-rigid transformation of 3D coordinates 3dAnatNudgeTry to align EPI and structural volumes automatically plugin: Nudge DatasetAlign EPI and structural volumes manually 3dTagalignAlign datasets by matching manually placed ‘tags’ plugin: Edit TagsetPlace ‘tags’ in a dataset interactively adwarpTransform dataset using warp from dataset header VecwarpTransform 3-vectors using warp from dataset header Dataset File Manipulation 3dcopyCopy a dataset to make new files 3drenameRename dataset files 3ddupMake an ‘empty’ duplicate (warp-on-demand) of a dataset ROI Generation and Usage Programs plugin: Draw DatasetManually draw ROI mask datasets 3dAutomaskGenerate a brain-only mask from an EPI dataset 3dmaskaveCalculate dataset values averaged over a ROI 3dmaskdumpOutput all dataset values in a ROI 3dROIstatsCalculate dataset values from multiple ROIs 3dUndumpInput text values into a dataset (inverse of 3dmaskdump) 3dOverlapCreate mask that is overlap of nonzero voxels from multiple datasets 3dfractionizeResample a mask dataset to a different resolution whereamiGet atlas region name for coordinates

6 -6- Simple Calculations on Datasets, Producing New Datasets 3dcalcVoxel-by-voxel general purpose calculator 3dmergeVarious spatial filters, thresholds, and averaging 3dTstatVarious statistics of multi-brick datasets, voxel-by-voxel 3dMeanAverage datasets together, voxel-by-voxel, for each timept 3dMax Simple statistics (max, min, mean) for scripts 3dWinsorNonlinear order statistics filter for spatial smoothing 3danisosmooth Edge preserving filter for spatial smoothing 3dLocalstat Find simple statistical values for neighborhoods around each voxel Computation of Various Numbers from Datasets 3ddotDot product (correlation coefficient) of 2 sub-bricks 3dclustFind connected clusters of nonzero voxels 3dExtremaFind local maxima (or minima) of datasets 3dFWHMEstimate Full Width Half Max of dataset spatial correlation 3dMaxFind range of voxel values (max, min, count) in a dataset 3dDWItoDTCompute diffusion tensor,eigenvalues from DWI data 3dDTeigCompute eigenvalues from diffusion tensor data

7 -7- Simulated Dataset Generators 3dTSgenGenerate 3D+time dataset from 1D model and noise AlphaSimSimulate datasets and estimate statistical power 3dConvolveSimulate datasets via convolution Programs for Dealing with 1D Time Series 1dcatCatenate them horizontally 1deval1D calculator (like 3dcalc for 1D files) 1dplotGraph values from columns in a file 1dgrayplotShow values from columns in a file as bands of gray levels 1dtransposeTranspose them (interchange rows and columns) Image Registration Programs 3dvolregVolumetric registration (rigid body in 3D) 3dWarpDriveEnhanced volumetric registration, includes warping 3dImRegSlice-by-slice registration (rigid body in 2D)

8 -8- Miscellaneous File Manipulations 2swapByte pair swap: ab ba 4swapByte quad swap: abc dcba 24swapMixed 2 and 4 byte swaps in same file strblastFind a string in a file and replace it with junk Miscellaneous Utilities byteorderReport the byteorder of the current CPU ccalcA command line calculator (like 3dcalc) cdfCompute probabilities, thresholds for standard distributions countGenerate numbered strings for command line scripts Image File Header Printouts dicom_hdrPrint information from a DICOM file ge_headerPrint information from a GE I. file mayo_analyzePrint information froman ANALYZE.hdr file siemens_visionPrint information from a Siemens Vision.ima file Miscellaneous Visualization Tools aivAFNI Image Viewer program plugin: Render[new]Interactive volume rendering plugin: Dataset#NGraph extra dataset time series in AFNI graph viewer

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