Freeview from FreeSurfer

Freeview from FreeSurfer

FreeSurfer is an open source software package for the analysis and visualization of structural and functional neuroimaging data. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. It’s a really useful tool that allows for automated processes as well as manual interventions, mainly through it’s GUI, Freeview.

I started using FreeSurfer and Freeview last year and, albeit the documentation being quite thorough, I had a harder time navigating the website than I expected.

So here are a few tricks to make your handling FreeSurfer’s GUI, Freeview, easier and faster!

1. Starting Freeview

You can start freeview by just typing freeview in your command line and then opening the files you want. Of course, you will be far better off if you write a small script with your usual calls.

The command options available for Freeview are:

Argument Action
-v load a volume file
-l load a label file
-dti load one or more dti volumes
-f load a surface
-w load waypoints

I have the following script saved under my subjects/ folder:

export SUBJECT='<subject name>'
freeview -v \
    $SUBJECT/mri/T1.mgz \
    $SUBJECT/mri/wm.mgz \
    $SUBJECT/mri/brainmask.mgz \
    -f \
    $SUBJECT/surf/lh.white:edgecolor=blue \
    $SUBJECT/surf/lh.pial:edgecolor=yellow \
    $SUBJECT/surf/rh.white:edgecolor=blue \
    $SUBJECT/surf/rh.pial:edgecolor=yellow

So, if I want to analyze, let’s say, subject bert’s images, I just open my freeview.sh script with a text editor and change <subject name> to bert (which is this subject’s folder name). Then, I can open a terminal, navigate to my subjects/ folder and type:

./freeview.sh

For more information on how to use the freeview command, type:

freeview --help

You’ll get a list of the available sub-options to make the most out of your image visualization!

All right, we have opened Freeview and we’re ready to start interacting with the GUI!

2. Check out the available Freeview keyboard shortcuts!

This single trick will save you an amazing amount of time. I have been working with CentOs and a few shortcuts I have found by experimenting are:

Command Action
Alt + N Navigate Tool
Ctrl + E Recon Edit Tool
Alt + E Voxel Edit Tool
Ctrl + F Toggle all surfaces
Alt + C Alternate between volumes/surfaces
Ctrl + P Toggle left side menu
Ctrl + T Point set edit
Ctrl + R Reset View
Alt + X Show sagital images
Alt + Y Show axial images
Alt + Z Show coronal images
Alt + A/D Decrease/Increase opacity of currently highlighted volume
Ctrl + D Hide brainmask
Alt + F Toggle currently highlighted surface
Alt + U Show cursor

You’ll find other shortcuts under this link. I’ll copy the most useful ones here for convenience:

Command Action
Ctrl + S Save
Ctrl + Z Undo
Ctrl + Q Exit Freeview
Ctrl + O Load Volume
Up/Down Arrow Keys or PageUp/PageDown Change slice
Scroll or Drag-Right-Click Zoom In/Zoom Out
Ctrl + Up/Down/Left/Right (arrow keys) Moving volume (Panning)
Alt + V Toggle currently highlighted volume
Shift-Drag Left Click Adjust Contrast/Brightness
Zoom in at current location Ctrl-Left-Click (or scroll)
Zoom out at current location Ctrl-Right-Click (or scroll)

When you’re in Voxel/Recon/ROI edit mode:

Command Action
Draw / Fill Left Click
Erase / Erase Fill Shift+Left Click

That concludes this short tutorial about Freeview! If you want to read/know more, the full Freeview Guide can be found here. Also, check out this cool Freeview demo.

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Physician and Computational neuroscientist

My research interests include using modeling approaches to better understand neurological and psychiatric diseases. Views expressed are my own.