# Command list and man pages

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

man -M camino/man <command>.

You can avoid having to type the -M part by doing

export MANPATH=/path/to/camino/man:$MANPATH

Then you can just type

man <command>.

Additional general technical documentation can be found at the Technical Documentation page on the sidebar.

adcfit - Fits the apparent diffusion coefficient to diffusion MRI

addnoise - Adds noise to diffusion MRI measurements.

analyze2voxel - Converts scanner-order data in Analyze format to voxel-order data.

analyzedti - Takes Analyze format raw data and outputs DT data in Analyze format

analyzeheader - Create or read an Analyze 7.5 header file.

averagedwi - Average some or all of the DWI data.

axialdistfit - Fits an axial PDF to sets of axes.

ballstickfit - Fits a partial volume model to diffusion MRI measurements.

byte2txt - Converts binary byte data to text.

camino - Overview of the Camino diffusion MR reconstuction toolkit.

cbsmat - Computes connectivity-based segmentation of a seed image.

char2txt - Converts binary char data to text.

combinetwofibreluts - Combine two fibre LUTs with a range of

conmat - Computes connectivity matrices from streamlines.

consfrac - Computes the consistency fraction for multiple fibre reconstructions.

countseeds - Counts seed voxels within an image.

counttracts - Counts tracts in a Bfloat file.

datastats - Computes simple statistics of each diffusion weighted measurement within a region of interest.

datasynth - Generates synthetic diffusion MRI data.

double2txt - Converts big-endian binary double data to text.

dt2mha - Converts Camino tensors to mha files.

dt2nii - Converts Camino tensors to nii files.

dteig - Computes the eigensystem of tensors.

dtfit - Fits the diffusion tensor to diffusion MRI measurements.

dtlutgen - Generates a PICo lookup table (LUT) or tables.

dtmx - Creates a linear transform for fitting the diffusion tensor.

dtpdview - Visualizes principal directions of diffusion tensors

dtshape - Computes DT shape statistics.

estimatesnr - Estimates the signal to noise ratio in b=0 images.

fa - Computes the fractional anisotropy of tensors.

FanningGrid- Creates a voxel grid simulating fanning structure.

float2txt - Converts big-endian binary float data to text.

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

image2voxel - Converts scanner-order data in a supported image format to voxel-order data.

imagestats - Computes voxelwise statistics on sets of images.

int2txt - Converts big-endian binary integer data to text.

invstats - Computes statistics of populations of diffusion tensors.

linrecon - Runs a linear transformation in each voxel.

long2txt - Converts big-endian binary long integer data to text.

mask - Creates a background mask from a voxel-ordered DW data file by

mbalign - Aligns the diffusion-weighted images within a single acquisition.

md - Computes the mean diffusivity (trace/3) from diffusion tensors.

mesd - Maximum entropy spherical deconvolution.

mfrstats - Computes statistics of populations of multiple fibre directions.

mha2dt - Converts MetaIO tensors to Camino.

modelfit - Fits models of the spin-displacement density to diffusion MRI measurements.

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

nii2dt - Converts NIFTI-1 tensors to Camino.

niftiheader - Read a NIFTI-1 header and print the header attributes.

orderpoints - Order points such that a partial scan has evenly spaced gradient directions

orientbiasmap - Evaluate point sets for orientation bias and variance in DTI parameters.

pdview - Visualizes principal direction(s) in each voxel

picocalibdata - Creates synthetic data for PICo calibration

picopdfs - Gets the parameters of a PICo PDF for an image.

pointset2scheme - Creates scheme files from point sets.

procstreamlines - Process streamline data

qballmx - Creates a reconstruction matrix for Q-Ball

reorient - Reorients diffusion tensors for consistency with an image transformation.

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

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

scanner2voxel - Converts scanner-order data to voxel-order data.

scheme2fsl - Reads a Camino V0 scheme file and writes FSL bvecs and bvals files.

selectshells - Subset DWI data by selecting shells in a specified range of b-values.

sfanis - Computes an index of anisotropy of spherical functions.

sfkurtosis - Computes an index of kurtosis of spherical functions.

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

sfpeaks - Finds the peaks of spherical functions.

sfpicocalibdata - Generates Spherical Function PICo Calibration Data

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

sfskewness - Computes an index of skewness of spherical functions.

shfit - Fits the spherical harmonic series to the log measurements.

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

short2txt - Converts big-endian binary short integer data to text.

shredder - Extracts periodic chunks from a data stream.

split4dnii - Converts 4D or 5D NIFTI-1 files to 3D volumes.

subsetpoints - Order points into subsets such that each subset has evenly spaced gradient directions

subsetscheme - Create scheme files from a subset of directions in an existing scheme

targetprobs2txt - Converts results of connectivity based segmentation to a text file.

threetenfit - Fits three diffusion tensors to diffusion MRI measurements.

track - Performs streamline tractography.

shredder Extracts bunches of streamlines.

tractstatimage - Computes images based on statistics from streamline tracts.

tractstats - Computes statistics from streamline tracts.

trd - Computes the trace of tensors.

twotenfit - Fits two diffusion tensors to diffusion MRI measurements.

vcthreshselect - Visualizes F-test data from voxelclassify(1).

voxel2image - Converts raw data to images.

voxel2scanner - Converts voxel-order data to scanner-order data.

voxelclassify - Classifies voxels according to the lowest-order spherical

voxelmean - calculates the mean of each diffusion MRI measurement in a set of voxels.

vtkstreamlines - Convert streamlines to VTK

wdtfit - Fits the diffusion tensor to diffusion MRI measurements.