Introduction to FreeSurfer Output

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This quiz relates to the content in the FreeSurfer tutorial titled Introduction of FreeSurfer Output (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview).

By the end of that tutorial, you should know:
1. How to visualize and inspect FreeSurfer data
2. The command to visualize data in Freeview
3. What to look for when visualizing data including that surfaces follow the gray and white matter boundaries and that the aseg.mgz accurately follows the subcortical intensity boundaries
4. The regions that are not intended to be accurate and that these inaccuracies can be ignored as subcortical regions are excluded from cortical measures
5. Which surfaces can be viewed in 3D

Name (optional)

Are you in the FreeSurfer course? *

Yes

What is the input for FreeSurfer?

1 point

A T1-weighted (MPRAGE) image, 2mm isotropic

A T1-weighted (MPRAGE) image, 1mm isotropic

A T2-weighted image, 1mm isotropic

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Fill in the blank: A _________ is a reconstructed boundary.

1 point

Label

Surface

Volume

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Fill in the blank: A ________ is a 3D dataset that typically contains either intensity information from the original MRI or the results of segmenting the data into tissue classes.

1 point

Surface

Volume

Label

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What are the three most common volumes and what do they contain?

5 points

skull stripped volume primarily used for troubleshooting

white matter mask also used for troubleshooting

subcortical segmentation volume

Not one of the three most common volumes

brainmask.mgz

brain.mgz

wm.mgz

aseg.mgz

orig.mgz

Which surface(s) can be viewed in 3D?

1 point

Pial surface

White surface

Inflated surface

All of the above

None of the above

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Where are surfaces not intended to be accurate?

1 point

Areas around the midline

Areas around the occipital lobe

Areas around the hippocampus and amygdala

Areas around the temporal lobe

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What is the command for opening surfaces and volumes in Freeview?

1 point

freesurfer -v /path/to/volume/data -s /path/to/surface/data

freeview -v /path/to/volume/data -s /path/to/surface/data

freesurfer -v /path/to/volume/data -f /path/to/suface/data

freeview -v /path/to/volume/data -f /path/to/surface/data

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Using the "--help" flag as a resources, how might you open volume brainmask.mgz at coordinates 175, 105, 145? Assume that you are already in the mri directory.

Hint: Include the entire command line

1 point

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