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| setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons | export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons |
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| === 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! |
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| There are three steps in the TRACULA processing stream (which is called by the command {{{trac-all}}}): *Pre-processing *FSL's {{{bedpostX}}} *Reconstructing white-matter (WM) pathways '''For NMR-Center-Users Only''' * ''Do not submit trac-all as a command in the cluster but run it on the command line. It will submit each subject listed in the [[FsTutorial/Tracula|Configuration File]] file as a seperate job to the cluster.'' Below, we show you how to run these steps:. <<BR>> '''Warning''': Running trac-all comands can take a significant amount of time. Therefore '''do not run''' the commands in this sections. All the data has already been processed for you! |
There are three steps involved in processing individual subjects with TRACULA: * Pre-processing * FSL's {{{bedpostX}}} * Reconstructing white-matter pathways The three steps must be run in this order, using the command {{{trac-all.}}} * '''Martinos Center users:''' Do not submit {{{trac-all}}} as a job on the cluster using pbsubmit. Instead, run {{{trac-all}}} directly on the command line. If run on the cluster, {{{trac-all}}} will submit each subject listed in the [[FsTutorial/Tracula|configuration file]] as a seperate job on the cluster. |
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| Some pre-processing of the diffusion image data is needed before WM pathways can be reconstructed by TRACULA. Specifically, these pre-processing steps are: *Eddy-current correction *Intra-subject registration (diffusion data to T1) *Inter-subject registration (individual subject to a common space) *Creation of cortical and white-matter masks from FreeSurfer recons *Tensor fitting (using FSL's {{{dtifit}}}) *Computing anatomical priors for WM pathways from training data All of the above pre-processing steps can be run by passing the {{{-prep}}} flag to {{{trac-all}}} as follows: |
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 * Computing measures of head motion during the DWI scan * 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 extraction 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: {{{#!wiki caution '''Do not run this command if you're at an organized course.''' It will take a while and has already been done for you. }}} |
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| trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject | trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial |
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| The {{{-c}}} flag calls your configuration file (described [[FsTutorial/Tracula|here]]) which contains your preferences for these pre-processing steps (i.e. CVS vs. FLIRT for registration). == FSL's BedpostX == {{{BedpostX}}} is a program included in FSL that estimates probability distributions of the parameters of the ball-and-stick diffusion model at every voxel. The output of {{{bedpostX}}} (this voxel-wise probability information) is necessary for doing tractography on the subject. Passing the flag below will conveniently run {{{bedpostX}}} on the subjects specified in your configuration file now that all essential data was created in the pre-processing step: |
The argument of the {{{-c}}} command-line option is the [[FsTutorial/Tracula|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. This command will run {{{bedpostX}}} on the pre-processed data of all the subjects specified in the configuration file: |
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| trac-all -bedp -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject | trac-all -bedp -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial |
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| == Reconstructing WM Pathways == The last step is to generate the probability distributions for the set of major WM 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 which comes with TRACULA. To generate the WM pathways, you would run the following: |
== Reconstructing white-matter pathways == The final 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: |
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| trac-all -path -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject | trac-all -path -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial |
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| [[FsTutorial/Diffusion|Top]] | [[FsTutorial/Tracula|Previous]] | [[FsTutorial/TraculaOutputs|Next]] | [[FsTutorial|Top]] | [[FsTutorial/Tracula|Previous]] | [[FsTutorial/TraculaOutputs|Next]] |
Running TRACULA
Remember...
For each new terminal that you open, you must do:
export SUBJECTS_DIR=$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!
There are three steps involved in processing individual subjects with TRACULA:
- Pre-processing
FSL's bedpostX
- Reconstructing white-matter pathways
The three steps must be run in this order, using the command trac-all.
Martinos Center users: Do not submit trac-all as a job on the cluster using pbsubmit. Instead, run trac-all directly 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.
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
- Computing measures of head motion during the DWI scan
- 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 extraction 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:
Do not run this command 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. 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 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
Now let's look at the results! Click on Next below.