These are answers to the 'Study Questions'

Contents

  1. Inspection of Freesurfer Output
    1. What is the input for FreeSurfer?
    2. What is a volume and a surface?
    3. What are the three most common volumes and what do they contain?
    4. Which surfaces can be viewed in 3D?
    5. Which surfaces are not intended to be accurate? Why doesn’t this matter?
    6. What is the command for opening Freeview?
    7. Using the “--help” flag as a resource, how might you open volume brainmask.mgz at coordinates 175, 105, 145?
  2. ROI Analysis
    1. Which atlas does the aparc+aseg.mgz use? How do you view the other atlas?
    2. What are the commands needed to create and open a table of segmentation volumes with multiple subjects?
    3. What structure is #1035 on the look up table (LUT)? What number would you use to look up the Left-Caudate? How could you find this information using Unix? How could you find this information online?
  3. Group Analysis
    1. What is a contrast?
    2. Which type of file does FreeSurfer not automatically create? Why not?
    3. What colors are associated with a negative and positive correlation?
    4. What does the threshold of 4 mean? What would the threshold be if the p-value was < 0.001? What about < 0.05?

Inspection of Freesurfer Output

What is the input for FreeSurfer?

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

What is a volume and a surface?

A volume is a 3D data set that typically contains either intensity information from the original MRI or the results of segmenting the data into tissue classes. A surface is a reconstructed boundary.

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

1. brainmask.mgz : skull-stripped volume primarily used for troubleshooting

2. wm.mgz : white matter mask also used for troubleshooting

3. aseg.mgz : subcortical segmentation volume

Which surfaces can be viewed in 3D?

The pial, white, and inflated surfaces. The following are examples of overlays: sulcal and curvature maps, thickness maps, and cortical parcellation.

Which surfaces are not intended to be accurate? Why doesn’t this matter?

Areas around the hippocampus and amygdala, and around the midline cut. This doesn't matter because these are subcortical structures, they do not need to be defined by surfaces.

What is the command for opening Freeview?

Freeview -v /path/to/mri/dir -f /path/to/surf/dir

Using the “--help” flag as a resource, how might you open volume brainmask.mgz at coordinates 175, 105, 145?

freeview -v brainmask.mgz --slice 175 105 145

ROI Analysis

Which atlas does the aparc+aseg.mgz use? How do you view the other atlas?

The aparc+aseg.mgz uses the Desikan-Killiany atlas.To view the Destrieux atlas load <subjectname>/mri/aparc.a2009+aseg.mgz

What are the commands needed to create and open a table of segmentation volumes with multiple subjects?

asegstats2table - - subjects 004 021 040 067 080 092 (subject files) - - segno 11 17 18 (ROIs you wish to get stats on) - - tablefile aseg.vol.table less aseg.vol.table OR gedit aseg.vol.table

What structure is #1035 on the look up table (LUT)? What number would you use to look up the Left-Caudate? How could you find this information using Unix? How could you find this information online?

Structure #1035 is ctx-lh-insula. The number to look up the Left-Caudate is 11. This information can be found using Unix with the command "less $FREESURFER_HOME/FreeSurferColorLUT.txt" or online at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT.

Group Analysis

What is a contrast?

A vector that specifies the hypothesis we are testing.

Which type of file does FreeSurfer not automatically create? Why not?

The contrast matrix file is not automatically created by FreeSurfer because it depends on the hypothesis you want to test.

What colors are associated with a negative and positive correlation?

Blue indicates a negative correlation while red indicates a positive correlation.

What does the threshold of 4 mean? What would the threshold be if the p-value was < 0.001? What about < 0.05?

A threshold of 4 means vertices with p < 0.0001 uncorrected will have color. If the p-value was <0.001 then the threshold would be 3. If the p-value was <0.05 then the threshold would be 1.5.