Camino | Main / Tutorials

These tutorials are out of date, please see http://cmic.cs.ucl.ac.uk/camino for current tutorials and documentation.

While most of the current code is backwards compatible, some of the commands here may no longer work. Please see the current tutorials at the new site before emailing us with problems. Thanks.

Conversion of raw data from DICOM to NIfTI
NIfTI conversion to Camino raw format
Dealing with diffusion tensors in NIfTI format

Detecting Crossing Fibres in the post-mortem pig brain
Topics covered:

Creating FA map

Creating Tr(D) map

Creating colour-coded direction map

Detecting fibre crossings

Using camino to generate and use Q-Ball data
Topics covered:

Create a Q-Ball ODF map (grey scale and color)
Extracting useful information about the peaks of the Q-Ball ODFs
Visualising Q-Ball ODF fibre-orientation estimates

Tractography tutorial - generating and visualising results
Topics covered:

Viewing the colour-coded direction map with pdview

Using an ROI

Streamline Tractography

Probabilistic Tractography using PICo.

Parallel processing of PICo probability maps.

Tractography with q-ball and PASMRI
Topics covered:

Running reduced-encoding PASMRI
Deterministic tractography with PASMRI or q-ball
PICo calibration with PASMRI or q-ball
Probabilistic tractography with PASMRI or q-ball

Connectivity Mapping
Topics covered:

How to construct a connectivity matrix

Connectivity segmentation: more tractography operations
Topics covered:

PICo using waypoints and target ROIs

Segmenting brain structures by connectivity

Running PASMRI using parallel processing

Topics covered:

Running PASMRI using SGE
Creating PAS plots.

Using camino to produce synthetic data
Topics covered:

Synthetic data from 3D Gaussian functions
Synthetic data using Monte-Carlo simulation
Generating statistics on fibre orientation estimates
Constructing data files using shredder
Synthetic data for fibre-crossing studies

Spatial normalization and warping of tensor images
Topics covered:

Creating masked diffusion tensor images
Using flirt to compute affine transformations between images
Warping a diffusion tensor image
Reorienting diffusion tensors for consistency with the image transformation

Registering the DWIs within a single acquisition

Topics covered:

Preparation before running mbalign
Run mbalign
Improve performance
Update Gradient
More hints

Creating a general-waveform schemefile
Topics covered: What is a gen-wave?
Scheme-file format
Explanation of parameters

More advanced Monte-Carlo Simulations
This is intended as an overview of the capabilities of the Camino Monte-Carlo simulation. It contains sample commands for different substrates and describes other features of the simualtion that aren't documented elsewhere. Topics covered: Regular-packed cylinder substrates
Disordered, Gamma-distributed cylinder substrates
Crossing fibre substrates
Mesh substrates
Different scheme files
Permeability
Other measurement options

Mapping axon density and diameter with ActiveAx
Example data and data preparation.
Model fitting.
Generating parameter maps.