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Running TRACULA

Remember...

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

export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons
cd $TUTORIAL_DATA/diffusion_tutorial

If you are at an organized course

Running the commands described below will take more time than you have for this tutorial, so please DO NOT RUN these commands right now. All the data has already been processed for you!

If you are not at an organized course

If you are NOT taking one of the formally organized courses, then to follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. These are the commands that you need to run before getting started:

## bash
export FREESURFER_HOME=/path/to/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export TUTORIAL_DATA=<path_to_your_tutorial_data>
export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons
cd $SUBJECTS_DIR

## tcsh
setenv FREESURFER_HOME /path/to/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv TUTORIAL_DATA <path_to_your_tutorial_data>
setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons
cd $SUBJECTS_DIR

If you are not using the tutorial data you should set your SUBJECTS_DIR to the directory in which the recon(s) of the subject(s) you will use for this tutorial are located.

IMPORTANT: Check to make sure you have the latest version of FreeSurfer available before running this tutorial as Tracula is updated with new FreeSurfer version. To see the latest Tracula updates, click here.


There are three steps involved in processing individual subjects with TRACULA:

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

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:

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

Do not run these commands if you're at an organized course.

It will take a while and has already been done for you.

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

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

Ball-and-stick model fit

TRACULA uses the ball-and-stick model of diffusion to reconstruct the pathways from the DWI data. FSL's bedpostX fits the ball-and-stick model to the DWI data, estimating probability distributions of the parameters of this model at every voxel. bedpostx should only be run on a computer with high computational power, for more information on bedpostx click here. 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/dmrirc.tutorial

Reconstructing white-matter pathways

The final step is to generate the probability distributions for each of the 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/dmrirc.tutorial

TO CHECK THAT ALL FILES WERE GENERATED

See the trac-all page for a list of correct outputs for the -bedp and -path steps.

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


Summary

By the end of this page, you should know how to:

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FsTutorial/RunningTracula (last edited 2018-08-29 11:45:39 by EmmaBoyd)