Introduction to FreeSurfer Output
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”.
- Open the subject’s aparc+aseg.mgz volume with a colormap of “lut”.
- Swap the view to sagittal
- 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 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
Goal: Practice visualizing data with overlays.
- Open subj_004’s lh.pial surface, with the overlay names lh.thickness, set the overlay to display with a threshold of 1,2
- If needed, swap to the 3d view
- Find the orbitofrontal cortex (Look for a thin cortical area in the frontal lobe)
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 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
Goal: Practice opening multiple files at a time with FreeView.
- For this challenge start with this terminal command:
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 hand pial and white matter surfaces, alter it to open both for the right hand as well, with colors that match the left hand 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
Practice Working With Data
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 veriables 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 subjects 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.