These are answers to the 'Study Questions' in the FreeSurfer tutorials.

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?
    5. What was the DOF for this experiment?
    6. What was the FWHM?
    7. How many frames does beta have? Why? (hint: run mri_info on lh.gender_age.glmdir/beta.mgh)
  4. Clusterwise Correction for Multiple Comparisons
    1. Where is the information from the simulation stored?
    2. What are the steps for correcting for multiple comparisons after we have the distribution of maximum cluster size?
    3. When running a simulation, what does the line cwp 0.05 indicate? What value should be used to see all the clusters?
  5. QDEC
    1. What is the primary input to Qdec?
    2. What is Qdec designed to do?
    3. What are the necessary steps for preprocessing the data?
    4. What does FindClustersAndGotoMax on the Display tab do?
    5. What would you type into the terminal to map rh.occipital.label (created on fsaverage) onto subject 020?
  6. Troubleshooting your output
    1. What watershed parameter should be used to start if there is too much skull remaining? What if part of the brain is missing?
    2. Where should control points be placed?
    3. Which volume should you edit when the pial surface includes too much?
    4. Which volume should you edit when the error affects the white matter?
    5. What flag can you use with recon-all if you’re not sure where in the processing stream your edits begin?
    6. Where should you save control point files and what is the proper naming format?
    7. When viewing edits after running recon all, how can you check to see if your control points corrected any segmentation errors? What other files would you load?
    8. You’ve added control points and made brainmask edits to subject 005. What recon-all flags do you use? What does your command look like?
    9. When should brain.finalsurfs.manedit.mgz edits be made?
  7. Multimodal Analysis
    1. Which imaging plane(s) (axial/horizontal, sagittal, coronal) move on on the x axis when you drag the X (L-R) Translate bar?
    2. Which value in the register.dat.mincost file indicates the quality of the registration? What value should this be below?
    3. What is the first thing to check when processing fMRI data?
    4. What would you do if you wanted to run the negative functional constraint?
    5. What is the only step that is different from the anatomical analysis?
  8. Longitudinal Processing, Edits and Post-Processing
    1. What are the three processing steps and what do they mean?
    2. What happens if the across time registration fails?
    3. What is the best way to fix a skull strip error and where can this be edited?
    4. Which stages can control points be added to?
    5. Where should white matter edits be made?


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 

To view: 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.

What was the DOF for this experiment?

The degrees of freedom (DOF) for this experiment is 36.

What was the FWHM?

The full width half max (FWHM) of this experiment is 13.629911.

How many frames does beta have? Why? (hint: run mri_info on lh.gender_age.glmdir/beta.mgh)

This experiment has 4 frames because the experiment has an offset for each group and a slope for each group.

The number of frames relates to the number of modeled effects in the analysis. Eg, if you have two groups, then the number of frames will be two. If you have two groups plus age, then you will have 4 frames: an offset for each group and an age slope for each group. Like DOF and FWHM, this is not critical to understanding the analysis, it is just a way for them to connect the output to things they already understand about doing an analysis.


Clusterwise Correction for Multiple Comparisons

Where is the information from the simulation stored?

A simple text file called a CSD (Cluster Simulation Data) file.

What are the steps for correcting for multiple comparisons after we have the distribution of maximum cluster size?

1.Going back to the original data.

2.Thresholding using same level and sign.

3.Finding clusters in thresholded map.

4.For each cluster, p = probability of seeing a maximum cluster that size or larger during simulation.

When running a simulation, what does the line cwp 0.05 indicate? What value should be used to see all the clusters?

This means that clusters that have cluster-wise p-values of less than 0.05 will be kept. To see all the clusters set to .999.


QDEC

What is the primary input to Qdec?

A text file (qdec.table.dat) in the subjects directory that contains the subject IDs and discrete and continuous factors in table format.

What is Qdec designed to do?

Aid researchers in performing inter-subject and group averaging and interface on morphometry data. This is a GUI front end to the mri_glmfit binary which is used to model the data as a linear combination of effects related to variables of interest, confounds, and error.

What are the necessary steps for preprocessing the data?

Running recon-all (with the -qcache flag) for the group subject data - need to have fsaverage in the SUBJECTS_DIR. Creating the input for Qdec and saving it in the subjects directory

What does FindClustersAndGotoMax on the Display tab do?

It finds clusters based on the currently selected display threshold, outputs a table of results, and produces a plot based on the data.

What would you type into the terminal to map rh.occipital.label (created on fsaverage) onto subject 020?

mri_label2label --srclabel rh.occipital --srcsubject fsaverage --trgsubject 020 --trglabel rh.occipital --regmethod surface --hemi rh


Troubleshooting your output

What watershed parameter should be used to start if there is too much skull remaining? What if part of the brain is missing?

If there is too much skull remaining the watershed parameter should be 15 and if part of the brain is missing it should be 35.

Where should control points be placed?

Control points should be placed in areas of white matter that have a voxel intensity less than 110 and away from gray matter to avoid partial voluming.

Which volume should you edit when the pial surface includes too much?

You should edit the brainmask.mgz.

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

You should edit the wm.mgz.

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

You should run -all (note: this will run through the entire recon-all command) or -make all if using the development or 5.3 FreeSurfer versions.

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

You should save them in the subject’s tmp directory and name them control.dat.

When viewing edits after running recon all, how can you check to see if your control points corrected any segmentation errors? What other files would you load?

Load the control.dat file from the subjects tmp file over the newly edited brain to see if they had any effect. You can also load the wm.mgz, pial or white surface.

You’ve added control points and made brainmask edits to subject 005. What recon-all flags do you use? What does your command look like?

You should use the flags: -autorecon2-cp & -autorecon3. The command line would look like: recon-all -autorecon2-wm -autorecon3 -subjid 005

When should brain.finalsurfs.manedit.mgz edits be made?

When there are problems involving pial surface misplacement such as when parts of the pial surface have extended into the cerebellum in certain areas.


Multimodal Analysis

Which imaging plane(s) (axial/horizontal, sagittal, coronal) move on on the x axis when you drag the X (L-R) Translate bar?

The axial/horizontal & coronal imaging planes.

Which value in the register.dat.mincost file indicates the quality of the registration? What value should this be below?

The first value in the register.dat.mincost file indicates the quality of the registration. A value below 0.5 indicates a good registration.

What is the first thing to check when processing fMRI data?

The registration of the functional volume and the anatomical surfaces.

What would you do if you wanted to run the negative functional constraint?

You would need to change the masksign flag in mri_segstats to neg. (--masksign neg)

What is the only step that is different from the anatomical analysis?

The assembling the data is the only different step.


Longitudinal Processing, Edits and Post-Processing

What are the three processing steps and what do they mean?

1.CROSS - cross-sectional analysis and processing

2.BASE - creates the within subject template and the directory contains the results for the average anatomy of the subject across time

3.LONG - creates two longitudinal runs that create directories which contain the final and more reliable and accurate processing results

What happens if the across time registration fails?

The image will appear blurry or have ghosting.

What is the best way to fix a skull strip error and where can this be edited?

The best way is to adjust the watershed parameters on the cross-sectionals.

Which stages can control points be added to?

Control points can be used in any of the three stages.

Where should white matter edits be made?

White matter edits should be made to the wm.mgz on the base, however you can make changes to all of the stages.

FsTutorial/StudyQuestions (last edited 2018-08-21 10:59:48 by MorganFogarty)