These are answers to the diffusion related 'Study Questions'.

Contents

  1. Diffusion Analysis
    1. What happens if you try to run dt_recon more than one time?
    2. What does dt_recon do?
    3. What step should be completed after running dt_recon?
    4. What needs to be done in order to analyze specific subcortical and white matter regions in the diffusion data?

Diffusion Analysis

What happens if you try to run dt_recon more than one time?

You will receive and error that multiple volumes are found and the program will stop. This command can be run a second time after deleting the existing output directory and using a clean copy of the data.

What does dt_recon do?

This command accomplishes preprocessing of the data by correcting for eddy currents and motion artifacts and generates multiple NIFTI volumes.

What step should be completed after running dt_recon?

As always, you should check the registration to ensure that dt_recon was accurate in correcting for motion and eddy currents.

What needs to be done in order to analyze specific subcortical and white matter regions in the diffusion data?

The subcortical segmentations need to be resampled into the diffusion space using the ‘mri_vol2vol’ command