| Deletions are marked like this. | Additions are marked like this. |
| Line 118: | Line 118: |
|
---- = QDEC = <<Anchor(QdecInput)>> == What is the primary input to Qdec? == A text file which contains the subject IDs and discrete and continuous factors in table format. <<Anchor(QdecPurpose)>> == 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. <<Anchor(Preprocess)>> == What are the necessary steps for preprocessing the data? == Running recon-all for the group subject data - need to have fsaverage in the SUBJECTS_DIR Creating the text file input for Qdec <<Anchor(FindClusterAndGotoMax)>> == 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. <<Anchor(QdecCommand)>> == 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 |
These are answers to the 'Study Questions'
Contents
-
Inspection of Freesurfer Output
- What is the input for FreeSurfer?
- What is a volume and a surface?
- What are the three most common volumes and what do they contain?
- Which surfaces can be viewed in 3D?
- Which surfaces are not intended to be accurate? Why doesn’t this matter?
- What is the command for opening Freeview?
- Using the “--help” flag as a resource, how might you open volume brainmask.mgz at coordinates 175, 105, 145?
-
ROI Analysis
- Which atlas does the aparc+aseg.mgz use? How do you view the other atlas?
- What are the commands needed to create and open a table of segmentation volumes with multiple subjects?
- 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?
- Group Analysis
- Clusterwise Correction for Multiple Comparisons
- QDEC
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.
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 which 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 for the group subject data - need to have fsaverage in the SUBJECTS_DIR Creating the text file input for Qdec
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