Top | Previous | Next

Running TRACULA

Remember...

For each new terminal that you open, you must do:

setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons
cd $TUTORIAL_DATA/diffusion_tutorial

There are three steps in the TRACULA processing stream.

• Pre-processing

• FSL's bedpostX

• Reconstructing white-matter pathways

The three steps must be run in this order, using the command trac-all.

For NMR-Center-Users Only

• Do not submit trac-all as a job on the cluster. Instead, run trac-all on the command line. If run on the cluster, trac-all will submit each subject listed in the configuration file as a seperate job on the cluster.

Below, we show you how to run these steps:.

• Warning: Running trac-all can take a significant amount of time. Therefore do not run the commands in this section. All the data has already been processed for you!

Pre-processing

Some pre-processing of the diffusion image data is needed before white-matter pathways can be reconstructed by TRACULA. This pre-processing includes:

• Eddy-current compensation
• Intra-subject registration (individual DWI to individual T1)
• Inter-subject registration (individual T1 to a common template space)

• Creation of cortical and white-matter masks from FreeSurfer reconstructions

• Tensor fitting for extract of tensor-based measures (FA, MD, etc)
• Computing anatomical priors for white-matter pathways from the TRACULA atlas

All of the above pre-processing steps can be run by passing the -prep command-line option to trac-all as follows:

trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc.tutorial

The argument of the -c command-line option is the configuration file, where preferences for these pre-processing steps can be specified.

FSL's BedpostX

TRACULA uses the ball-and-stick model of diffusion to reconstruct the pathways from the DWI data. FSL's bedpostX fit the ball-and-stick model to the DWI data, estimating probability distributions of the parameters this model at every voxel. This command will run bedpostX on the pre-processed data of all the subjects specified in the configuration file:

trac-all -bedp -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc.tutorial

Reconstructing White Matter Pathways

The last step is to generate the probability distributions for each white-matter bundles you specified in the configuration file. This is done by simultaneously fitting the shape of each pathway to the results of the ball-and-stick model of diffusion from above and to the prior knowledge of the pathway anatomy given by the set of manually labeled training subjects in the TRACULA atlas. The following command will reconstruct the probabilistic distribution of the pathways:

trac-all -path -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc.tutorial

Now let's look at the results! Click on Next below.

Top | Previous | Next