Quickly inspect FreeSurfer cortical surfaces

To quickly inspect the surface reconstruction and parcellations produced by the cortical stream of FreeSurfer, rather than laboriously open each hemisphere at a time in tksurfer, an easier solution is to run a script that captures images, organise and present them all in a single html page that can be seen in any browser.

Before you start

Before you start, make sure you have:

  • FreeSurfer, any version released in the last 2 years. The procedure has been tested up to version 5.1.0.
  • ImageMagick, any recent version. For most Linux, ImageMagick can be installed directly from the distro’s repository. For Mac, it can be obtained with MacPorts or Fink.
  • The scripts takeshots, makehtml, shots_tksurfer.tcl, and shots_tkmedit.tcl. Put all these scripts into the same directory and make takeshots and makehtml executable.

Capturing the images

  1. Make sure recon-all finished for all your subjects. If there are no results, obviously there won’t be anything to inspect.
  2. Make sure the variable SUBJECTS_DIR is correctly set, pointing to the directory that contains the subjects, and that you have writing permissions to this directory.
  3. Prepare a text file containing a list of subjects, one per line, like this:
  4. Run the takeshots script. A typical usage is like this:
    ./takeshots -l listsubj.txt -m pial -m inflated -p aparc
    The options are:
    -l: List of subjects.
    -s: Additional subjects not in the list.
    -m: Surfaces to inspect (pial, inflated, white, sphere, etc).
    -p: Parcellations to inspect (aparc, aparc.a2005s, aparc.a2009s, etc).
    This script will create a subdirectory called ‘shots’ inside the directory of each subject, and will store a number of .tif files that are the different views of the cortical surfaces.
  5. Run the makehtml script. A typical usage is like this:
    ./makehtml -l listsubj.txt -m pial -m inflated -p aparc -d /path/to/html
    The options are identical to the previous command, with the addition of the option -d that lets you specify a directory where the html will be created. If this directory doesn’t exist, it will be created.

What you get

Open the file index.html in the directory specified in the previous step. There you’ll see all the surfaces of all the subjects, all in the same page, allowing you to quickly compare and have an idea of how good or bad they are. To see the name of the subject, hover the mouse on the corresponding image. Click on the image to see it larger. An example, using only pial and inflated surfaces, and the aparc parcellation, is here.