TRACULA

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TRACULA

This quiz relates to the content in the FreeSurfer tutorial titled TRACULA Tutorial (http://freesurfer.net/fswiki/FsTutorial/Tracula)

By the end of this tutorial, you should know how to:
1. Create a configuration file
2. Supply the correct steps/parameters for processing
3. Set additional options depending on the specifics of your analysis
4. Run Tracula (3 commands)
5. Check that all files were generated
6. Check head motion measures
7. View tensor fit outputs (in Freeview) in native space and MNI space
8. Check registration of tensor fit outputs (e.g, FA) to MNI space
9. Visualize and manipulate tractography outputs (in Freeview)
10. Extract 2 types of statistics on anisotropy and diffusivity measures for the white-matter pathways
11. Combine stats measures into tables for group analysis
12. Visualize your statistical analysis (in Freeview) along each pathway.

Name (optional)

Are you in the FreeSurfer course? *

Yes

In the configuration file, which command do you use to specify a b-value table for all scans?

1 point

bvallist

bvecfile

bvalfile

bveclist

Clear selection

You are required to create a configuration file to run TRACULA.

1 point

True

False

Clear selection

What are the steps involved in processing individual subjects with TRACULA?

1 point

Pre-processing

Reconstructing white matter pathways

FSL's bedpostX

Which model of diffusion does TRACULA use to reconstruct pathways from the DWI data?

1 point

The ball-and-stick model

The tensor model

Clear selection

What command is used to run the TRACULA processing steps?

1 point

recon-all

trac-all

tracula-all

Clear selection

Which command is used to fit the ball-and-stick model to the DWI data, estimating probability distributions of the parameters of this model at every voxel?

1 point

trac-all -prep -c /path/to/configuration/file

trac-all -bedp -c /path/to/configuration/file

trac-all -path -c /path/to/configuration/file

Clear selection

How does TRACULA assess for head motion in the DWI data?

1 point

The average volume-by-volume translation

The average volume-by-volume rotation

The percent of slices with excessive intensity drop-out

The average drop-out score for slice with excessive intensity drop-out

Which file contains these measures of motion?

Hint: Just list the file name, not the entire path.

1 point

Which flag is needed to open the merged 4D track volume in Freeview?

1 point

-v

-f

-t

-tv

Clear selection

pathstats.byvoxel.txt contains measures as a function of position along the trajectory of the pathway.

1 point

True

False

Clear selection

Which command do you need to use to convert the stats txt files for the tracts into tables that can be used for GLM analysis?

Hint: Write just the name of the command, not an entire command line.

1 point

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