Introduction to FreeSurfer Output DRAFT

Introduction to FreeSurfer Output

Exercise 1

Difficulty: Beginner

Goal: Practice basic Freeview tasks.

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?

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?

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 

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. MovieSetup.png

  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.


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.