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? 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:  freeview -f good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3 --viewport 3d 

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 

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

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:

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.