# Global tractography¶

## Introduction¶

Global tractography is the process of finding the full track configuration that best explains the measured DWI data. As opposed to streamline tracking, global tractography is less sensitive to noise, and the density of the resulting tractogram is directly related to the data at hand.

As of version 3.0, MRtrix supports global tractography using a multi-tissue spherical convolution model, as introduced in [Christiaens2015]. This method extends the method of [Reisert2011] to multi-shell response functions, estimated from the data, and adopts the multi-tissue model presented in [Jeurissen2014] to account for partial voluming.

## User guide¶

### Prerequisites¶

This global tractography implementation relies on multi-shell high angular resolution diffusion imaging (HARDI) data, containing at least 3 unique b-values (i.e 2 shells along with the b=0 volumes).

In addition, this command expects that suitable multi-shell multi-tissue response functions have already been computed. A number of approaches are available for this, please refer to the Response function estimation page for details.

### Invocation¶

For multi-shell DWI data, the most common use will be:

tckglobal dwi.mif wm_response.txt -riso csf_response.txt -riso gm_response.txt -mask mask.mif -niter 1e9 -fod fod.mif -fiso fiso.mif tracks.tck


In this example, dwi.mif is the input dataset, including the gradient table, and tracks.tck is the output tractogram. wm_response.txt, gm_response.txt and csf_response.txt are the corresponding tissue response functions (as estimated in a previous Response function estimation step). Optional output images fod.mif and fiso.mif contain the predicted WM fODF and isotropic tissue fractions of CSF and GM respectively, estimated as part of the global optimization and thus affected by spatial regularization.

#### Parameters¶

-niter: The number of iterations in the optimization. Although the default value is deliberately kept low, a full brain reconstruction will require at least 100 million iterations.

-lmax: Maximal order of the spherical harmonics basis.

-length: Length of each track segment (particle), which determines the resolution of the reconstruction.

-weight: Weight of each particle. Decreasing its value by a factor of two will roughly double the number of reconstructed tracks, albeit at increased computation time.

Particle potential -ppot: The particle potential essentially associates a cost to each particle, relative to its weight. As such, we are in fact trying to reconstruct the data as well as possible, with as few particles as needed. This ensures that there is sufficient proof for each individual particle, and hence avoids that a bit of noise in the data spurs generation of new (random) particles. Think of it as a parameter that balances sensitivity versus specificity. A higher particle potential requires more proof in the data and therefore leads to higher specificity; a smaller value increases sensitivity.

Connection potential -cpot: The connection potential is the driving force for connecting segments and hence building tracks. Higher values increase connectivity, at the cost of increased invalid connections.

#### Ancillary outputs¶

-fod: Outputs the predicted fibre orientation distribution function (fODF) as an image of spherical harmonics coefficients. This fODF is estimated as part of the global track optimization, and therefore incorporates the spatial regularization that it imposes. Internally, the fODF is represented as a discrete sum of apodized point spread functions (aPSF) oriented along the directions of all particles in the voxel, akin to track orientation distribution imaging (TODI, [Dhollander2014]). This internal representation is used to predict the DWI signal upon every change to the particle configuration.

-fiso: Outputs the estimated density of all isotropic tissue components, as multiple volumes in one 4-D image in the same order as their respective -riso kernels were provided.

-eext: Outputs the residual data energy image, including the L1-penalty imposed by the particle potential.