Command list and man pages

A general page reference for Camino file formats is [[Main.fileformats | here]]. The file formats are also documented in the relevant man pages below.

A general page reference for Camino file formats is [Main.fileformats | here]]. The file formats are also documented in the relevant man pages below.

This page contains a full list of Camino commands with links to HTML versions of each one's man page from the current Camino code. The man page for your particular version of the code may be viewed locally from a terminal by typing

(:title Command list and man pages:)
This page contains a full list of Camino commands with links to HTML versions of each ones man page. The pages may be viewed locally from a terminal by typing

man -M camino/man <command>.

[[man.adcfit | adcfit]] - Fits the apparent diffusion coefficient to diffusion MRI


[[man.addnoise | addnoise]] - Adds noise to diffusion MRI measurements.


[[man.analyze2voxel | analyze2voxel]] - Converts scanner-order data in Analyze format to voxel-order data.


[[man.analyzedti | analyzedti]] - Takes Analyze format raw data and outputs DT data in Analyze format


[[man.analyzeheader | analyzeheader]] - Create or read an Analyze 7.5 header file.


[[man.axialdistfit | axialdistfit]] - Fits an axial PDF to sets of axes.


[[man.ballstickfit | ballstickfit]] - Fits a partial volume model to diffusion MRI measurements.


[[man.byte2txt | byte2txt]] - Converts binary byte data to text.


[[man.camino | camino]] - Overview of the Camino diffusion MR reconstuction toolkit


[[man.char2txt | char2txt]] - Converts binary char data to text.


[[man.combinetwofibreluts | combinetwofibreluts]] - Combine two fibre LUTs with a range of


[[man.consfrac | consfrac]] - Computes the consistency fraction for multiple fibre reconstructions.


[[man.countseeds | countseeds]] - Counts seed voxels within an image.


[[man.cpstats | cpstats]] - Does statistics on PICo maps.


[[man.datastats | datastats]] - Computes simple statistics of each diffusion weighted measurement within a region of interest.


[[man.datasynth | datasynth]] - Generates synthetic diffusion MRI data.


[[man.double2txt | double2txt]] - Converts big-endian binary double data to text.


[[man.dt2nii | dt2nii]] - Converts Camino tensors to nii files.


[[man.dteig | dteig]] - Computes the eigensystem of tensors.


[[man.dtfit | dtfit]] - Fits the diffusion tensor to diffusion MRI measurements.


[[man.dtlutgen | dtlutgen]] - Generates a PICo lookup table (LUT) or tables.


[[man.dtmx | dtmx]] - Creates a linear transform for fitting the diffusion tensor.


[[man.dtpdview | dtpdview]] - Visualizes principal directions of diffusion tensors


[[man.dtshape | dtshape]] - Computes DT shape statistics.


[[man.estimatesnr | estimatesnr]] - Estimates the signal to noise ratio in b=0 images.


[[man.fa | fa]] - Computes the fractional anisotropy of tensors.


[[man.fanninggrid | FanningGrid ]]- Creates a voxel grid simulating fanning structure.


[[man.float2txt | float2txt]] - Converts big-endian binary float data to text.


[[man.fsl2scheme | fsl2scheme]] - converts b-vectors and b-values from FSL format to a Camino scheme file.


[[man.image2voxel | image2voxel]] - Converts scanner-order data in a supported image format to voxel-order data.


[[man.int2txt | int2txt]] - Converts big-endian binary integer data to text.


[[man.invstats | invstats]] - Computes statistics of populations of diffusion tensors.


[[man.linrecon | linrecon]] - Runs a linear transformation in each voxel.


[[man.long2txt | long2txt]] - Converts big-endian binary long integer data to text.


[[man.mask | mask]] - Creates a background mask from a voxel-ordered DW data file by


[[man.maxcp | maxcp]] - Computes the maximum connection probabilty over a region of interest.


[[man.mbalign | mbalign]] - Aligns the diffusion-weighted images within a single acquisition.


[[man.md | md]] - Computes the mean diffusivity (trace/3) from diffusion tensors.


[[man.meancp | meancp]] - Computes the mean connection probability over an ROI


[[man.mediancp | mediancp]] - Computes the median connection probability over an ROI


[[man.mesd | mesd]] - Maximum entropy spherical deconvolution.


[[man.metadt2camino | metadt2camino]] - Converts MetaIO tensors to Camino.


[[man.mfrstats | mfrstats]] - Computes statistics of populations of multiple fibre directions.


[[man.mincp | mincp]] - Computes the minimum connection probability over and ROI


[[man.modelfit | modelfit]] - Fits models of the spin-displacement density to diffusion MRI measurements.


[[man.multitenfit | multitenfit]] - Fits one or more diffusion tensors to the data in each voxel according to a voxel classification map to specify the number of


[[man.niftidt2camino | niftidt2camino]] - Converts NIFTI-1 tensors to Camino.


[[man.niftiheader | niftiheader]] - Read a NIFTI-1 header and print the header attributes.


[[man.orderpoints | orderpoints]] - Order points such that a partial scan has evenly spaced gradient directions


[[man.pdview | pdview]] - Visualizes principal direction(s) in each voxel


[[man.picocalibdata | picocalibdata]] - Creates synthetic data for PICo calibration


[[man.picopdfs | picopdfs]] - Gets the parameters of a PICo PDF for an image.


[[man.pointset2scheme | pointset2scheme]] - Creates scheme files from point sets.


[[man.pointset2scheme2 | pointset2scheme2]] - Creates version 2 scheme files from point sets.


[[man.procstreamlines | procstreamlines]] - Process streamline data


[[man.qballmx | qballmx]] - Creates a reconstruction matrix for Q-Ball


[[man.reorient | reorient]] - Reorients diffusion tensors for consistency with an image transformation.


[[man.restore | restore]] - Fits the diffusion tensor to diffusion MRI measurements robustly using the RESTORE algorithm by Chang et al MRM 53 2005.


[[man.rgbscalarimg | rgbscalarimg]] - Create an RGB image from diffusion peak directions, modulated by a scalar image (eg, anisotropy).


[[man.scanner2voxel | scanner2voxel]] - Converts scanner-order data to voxel-order data.


[[man.scheme2fsl | scheme2fsl]] - Reads a Camino V0 scheme file and writes FSL bvecs and bvals files.


[[man.sfanis | sfanis]] - Computes an index of anisotropy of spherical functions.


[[man.sfkurtosis | sfkurtosis]] - Computes an index of kurtosis of spherical functions.


[[man.sflutgen | sflutgen]] - Generates PICo lookup tables (LUT) for multi-fibre methods such as PASMRI and Q-Ball.


[[man.sfpeaks | sfpeaks]] - Finds the peaks of spherical functions.


[[man.sfpicocalibdata | sfpicocalibdata]] - Generates Spherical Function PICo Calibration Data


[[man.sfplot | sfplot]] - Plots the output of various diffusion MRI reconstruction algorithms over slices through data sets.


[[man.sfskewness | sfskewness]] - Computes an index of skewness of spherical functions.


[[man.shfit | shfit]] - Fits the spherical harmonic series to the log measurements.


[[man.shformatconverter | shformatconverter]] - Converts spherical harmonics from third party programs into the format used by camino.


[[man.short2txt | short2txt]] - Converts big-endian binary short integer data to text.


[[man.shredder | shredder]] - Extracts periodic chunks from a data stream.


[[man.split4dnii | split4dnii]] - Converts 4D or 5D NIFTI-1 files to 3D volumes.


[[man.subsetpoints | subsetpoints]] - Order points into subsets such that each subset has evenly spaced gradient directions


[[man.subsetscheme | subsetscheme]] - Create scheme files from a subset of directions in an existing scheme


[[man.targetprobs2txt | targetprobs2txt]] - Converts results of connectivity based segmentation to a text file.


[[man.threetenfit | threetenfit]] - Fits three diffusion tensors to diffusion MRI measurements.


[[man.track | track]] - Performs streamline tractography.


[[man.tractshredder | shredder]] Extracts bunches of streamlines.


[[man.tractstatimage | tractstatimage]] - Computes images based on statistics from streamline tracts.


[[man.tractstats | tractstats]] - Computes statistics from streamline tracts.


[[man.trd | trd]] - Computes the trace of tensors.


[[man.twotenfit | twotenfit]] - Fits two diffusion tensors to diffusion MRI measurements.


[[man.vcthreshselect | vcthreshselect]] - Visualizes F-test data from voxelclassify(1).


[[man.voxel2scanner | voxel2scanner]] - Converts voxel-order data to scanner-order data.


[[man.voxelclassify | voxelclassify]] - Classifies voxels according to the lowest-order spherical


[[man.voxelmean | voxelmean]] - calculates the mean of each diffusion MRI measurement in a set of voxels.


[[man.vtkstreamlines | vtkstreamlines]] - Convert streamlines to VTK


[[man.wdtfit | wdtfit]] - Fits the diffusion tensor to diffusion MRI measurements.