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# Introduction to FreeSurfer Output

### Exercise 1

Difficulty: Beginner

In the examples above you looked at data from a subject called “good_output”. For this challenge complete the following tasks for subject “subj_004”.

1. Open the subject’s aparc+aseg.mgz volume with a colormap of “lut”.
2. Swap the view to sagittal
3. Navigate with the arrow keys to find the right putamen

Need a hint? Here is how you opened up a similar volume for the “good_output” subject:  freeview -v good_output/mri/aseg.mgz:colormap=lut

Please note that we were in the \$TUTORIAL_DATA/buckner_data/tutorial_subjs directory when we used that command - so  cd  there if you'd like to base your command off the above example.

Want to know the answer? Click and drag to highlight and reveal the text below.

 freeview -v sub_004/mri/aparc+aseg.mgz:colormap=lut

### Exercise 2

Difficulty: Beginner

Goal: Practice visualizing data with overlays.

1. Open subj_004’s lh.pial surface, with the overlay named lh.thickness, set the overlay to display with a threshold of 1,2
2. Look up vertex 141813
3. What is the thickness and label of this vertex?

Need a hint? Here is how you opened up a similar surface for the good_output subject, with thickness information:  freeview -f good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3 --viewport 3d  And here is how you opened up a similar surface for the good_output subject with the Desikan-Killany parcellation:

Please note that we were in the \$TUTORIAL_DATA/buckner_data/tutorial_subjs directory when we used that command - so  cd  there if you'd like to base your command off the above example.

Want to know the answer? Click and drag to highlight and reveal the text below.

 freeview -v subj_004/surf/lh.pial:overlay=lh.thickness:overlay_threshold=1,2 --viewport 3d

### Exercise 3

Difficulty: Beginner

Goal: Practice opening multiple files at a time with FreeView.

freeview -v 004/mri/wm.mgz:colormap=jet 004/mri/brainmask.mgz -f 004/surf/lh.pial:edgecolor=blue 004/surf/lh.white:edgecolor=red

• Right now it only opens the left hemisphere pial and white matter surfaces, alter it to open both for the right hemisphere as well, with colors that match the left hemisphere side.
• Once you have the last command working, rearrange the volume layers in freesurfer so that the wm.mgz is at %20 opacity and the brainmask can be seen underneath it (this can also be done through altering the terminal command - you can choose which way to do so).

Want the solution? Click and drag to highlight and reveal the text below.

 freeview -v 004/mri/brainmask.mgz 004/mri/wm.mgz:colormap=jet:opacity=.2 -f 004/surf/lh.pial:edgecolor=blue 004/surf/lh.white:edgecolor=red 004/surf/rh.pial:edgecolor=blue 004/surf/rh.white:edgecolor=red

### Exercise 4

Difficulty: Intermediate - assumes some comfort with navigating Unix and FreeView

Goal: Export a series of images from FreeView and stitch them together to create a GIF.

1. Open up any surface from the tutorial data
2. Set the viewport to 3d view, right click in the viewport and select  Hide All Slices

3. In the  File  menu, select  Save Movie Frames

4. Set up the options as in the following picture - you will likely want to create a new directory in your home directory to save the output to.

5. In a terminal, navigate to the new directory you output the movie data to.
6. Run this command:  convert -delay .1 *.png brainanim.gif

• Note: convert is from the ImageMagick library, which is a prerequesite for running FreeView.

•  -delay  determines the gap between frames,  *.png  selects all png files in the working directory,  brainanim.gif  is the output name.

7. To view your GIF, open it with firefox  firefox brainanim.gif

# Practice Working With Data

### Exercise 1

Difficulty: Beginner

Goal: Prepare a dicom series for the recon-all stream

Your goal is to take a series of dicom images and set up your terminal variables and recon-all command to process them.

To begin navigate to the following directory in your terminal:  \$TUTORIAL_DATA/practice_with_dicoms

Take a look at the directories found there. The  dicoms  directory contains a dicom series, and the  work  directory is where your recon-all subject output should go.

Hints:

• Follow the tutorial example for guidance
• You will want to use dcmunpack to find the correct T1 weighted image to provide as input to recon-all
• Ensure you set your SUBJECTS_DIR variable to the  work  directory

When you believe everything is setup properly - run the recon-all command. Ensure that it starts without error, then use ctrl+c to cancel it. Check in the  work  directory to ensure a directory with your subject's name was created. If you are at a FreeSurfer course there won't be enough time for the recon-all command to complete, but if you are working on your own you are welcome to let the command finish and check out the outputs.

DraftChallenges (last edited 2019-10-28 13:17:59 by MatthewLarrabee)