List of COMEDI commands

Lang	Command	Dependence	Synopsis
	cmdDwiFiberClustering		White matter tractography clustering
	cmdDwiFiberDecode		White fiber streamline decoding using the cosine basis functions
	cmdDwiFiberFilter		Perform various editing operations on White fiber streamline
	cmdDwiFiberEncode		White fiber streamline encoding using the cosine basis functions
	cmdDwiFiberSmooth		White fiber streamline smoothing
	cmdDwiFiberStatis		Calculate statistics on streamlines
	cmdDwiGibbsRemoval		Remove Gibbs Ringing Artifacts from a DWI dataset
	cmdDwiNoiseRemoval		dMRI noise level estimation and denoising
	cmdDwiShellExtract		Extract diffusion-weighted volumes or certain shells from a DWI dataset
	cmdDwiShellMath		Apply an operation to each b-value shell in a DWI series
	cmdDwiSkullStripping		Generates a whole brain mask from a DWI image
	cmdFileConvert		Perform conversion between different file types
	cmdImageCompare		Computes a dissimilarity metric between two images
	cmdImageMath		Apply generic voxel-wise mathematical operations to images
	cmdImageRegister		Register two images together using a symmetric rigid, affine or non-linear transformation model
	cmdImageConcatenate		Concatenate several images into one
	cmdAnatGibbsRemoval		Remove Gibbs Ringing Artifacts from image
	cmdAnatHistogramMatch		Modify the intensities of one image to match the histogram of another
	cmdAnatHistogramMath		Generate a histogram of image intensities
	cmdImageCrop		Modify the grid of an image by cropping
	cmdImageFilter		Perform filtering operations on 3D / 4D MR images
	cmdImagePadding		Modify the grid of an image by padding
	cmdImageRegrid		Modify the grid of an image by regriding
	cmdAnatLabelConvert		Convert a connectome node image from one lookup table to another
	cmdAnatLabelFilter		Perform filtering operations on 3D / 4D mask images
	cmdAnatTissueSegment		Generate a set of tissue map
	cmdBidsLoad		Conversion of computational medical file
	cmdDwiBiasCorrect		Perform B1 field inhomogeneity correction for a DWI volume series
	cmdDwiConnectomeEstimate		Generate a connectome matrix from a streamlines file and a parcellation image
	cmdDwiConnectomeNormalize		Normalization or filtering of connectome matrix
	cmdDwiConnectomeExtract		Extract streamlines from a tractogram based on their assignment to parcellated nodes
	cmdDwiDirectionSampling		Generate a set of uniformly distributed directions on single-/multi-shell using a bipolar electrostatic repulsion model
	cmdDwiDirectionSplit		Split a set of evenly distributed directions into approximately uniformly distributed subsets
	cmdDwiEddyCorrect		Perform diffusion image pre-processing using FSL’s eddy tool; including inhomogeneity distortion correction using FSL’s topup tool if possible
	cmdDwiFiberMapping		Use track data as a form of contrast for producing a high-resolution image
	cmdDwiFiberMeasure		Sample values of an associated image along tracks
	cmdDwiFiberRegister		Direct bundle registration
	cmdDwiFiberResample		Resample each streamline in a track file to a new set of vertices
	cmdDwiFiberSplit		Perform various editing operations on track files
	cmdDwiFiberTracking		Perform streamlines tractography
	cmdDwiFiberWarp		Apply a spatial transformation to a tracks file
	cmdDwiFodEstimate		Estimate fibre orientation distributions from diffusion data
	cmdDwiFodNormalize		Multi-tissue informed log-domain intensity normalisation
	cmdDwiFodPeaks		Extract the peaks of a spherical harmonic function in each voxel
	cmdDwiFodResponse		Estimate response function for spherical deconvolution
	cmdDwiFodRegister		Register the FOD image
	cmdDwiGradientCorrect		Check the orientation of the diffusion gradient table
	cmdDwiTensorEstimate		Diffusion tensor estimation
	cmdDwiKurtosisEstimate		Diffusion kurtosis estimation
	cmdDwiTissueSegment		Tissue segmentation ssing sparse non-negative matrix factorization of spherical mean diffusion MRI data
	cmdInfo		Display file header information
	cmdViewer		COMEDI viewer
	cmdClean		Clean up residual temporary files
	cmdInstall		Installation of COMEDI
	cmdSetup		Set up COMEDI
	cmdUpdate		Update COMEDI
	cmdDwiFiberFilterWithCommit		Filter a whole-brain fibre-tracking data set using COMMIT
	cmdDwiFiberTrackingWithDipy		Perform streamlines tractography using DIPY
	cmdInstallDipy		Installation of DIPY
	cmdInstallAmico		Installation of AMICO
	cmdInstallFsl		Installation of FSL
	cmdInstallMrtrix		Installation of MRtrix
	cmdInstallFreesurfer		Installation of Freesurfer
	cmdInstallAnts		Installation of ANTs
	cmdInstallCommit		Installation of COMMIT