Troubleshooting your FreeSurfer Output

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This quiz relates to the content in the FreeSurfer tutorial titled Troubleshooting FreeSurfer Output (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0)

Name (optional)

Are you in the FreeSurfer course? *

Yes

Your recon-all.log file says that your recon finished without error, do you still need to manually check your data?

1 point

Yes

Clear selection

What watershed parameter should be used to start if there is too much skull remaining?

1 point

Clear selection

What watershed parameter should be used to start if part of the brain is missing?

1 point

Clear selection

Where should control points be placed?

1 point

In areas of gray matter with an intensity of more than 110

In areas of white matter with an intensity of less than 110

On the border of white and gray matter

On the border of gray matter and CSF

Clear selection

Which volume should you edit when the pial surface is inaccurate?

1 point

brainmask.mgz

wm.mgz

aseg.mgz

orig.mgz

Clear selection

Which volumes should you edit when the error affects the white matter?

1 point

brainmask.mgz

wm.mgz

aseg.mgz

orig.mgz

Clear selection

You've added control points and made brainmask edits to subject 005. What does your command look like if you run it from the mri directory?

1 point

Where should you save control point files and what is the proper naming format?

1 point

The subject's label directory with the file named control.dat

The subject's tmp directory with the file named points.dat

The subject's temp directory with the file named control.dat

The subject's label directory with the file named points.dat

Clear selection

What flag can you use with recon-all if you're not sure where in the processing stream your edits begin?

1 point

recon-all -make all

recon-all -do all

recon-all -make-all

recon-all --all

Clear selection

Which flag can you use if you've made edits to your subject and no longer want to use them?

1 point

For this image, which volume would you edit to correct the errors in the green boxes?

1 point

wm.mgz

aseg.mgz

brainmask.mgz

Clear selection

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