Autorecon3
The third set of recon-all steps does an automated parcellation of the gyri and sulci of the cortical mesh (as described in this paper. It is invoked by calling recon-all -autorecon3. A shell script, autorecon3.sh has been created to simplify this step.
Run autorecon3.sh on a participant
autorecon3.sh 501
Some while later (about 90 minutes locally), the script will terminate and you can check out how well the parcellation turned out using tksurfer.
tksurfer 505_001 lh pial
Then File > Label > Import Annotation > Browse… > select corresponding ?h.aparc.annot file in that subject’s /label/ folder.
Here, the ‘?’ is a placeholder character, standing in for either ‘l’ or ‘r’, meaning you can select ‘rh.aparc.annot’ or ‘lh.aparc.annot’ (i.e., right or left hemisphere)
If you loaded the lh pial surface, you need to load the lh.aparc.annot. Similarly, if you loaded the rh pial surface, you need to load the rh.aparc.annot file.
Alternatively, you can load the cortical mesh and the labels simultaneously.
tksurfer -annot aparc 505_001 lh pial
If you select the wrong aparc.annot (e.g., selecting lh.aparc.annot when you have loaded the rh pial surface mesh, or if you load up the annotation table for a different participant), you will find your mesh gets a very interesting-looking, but utterly useless psychedelic color scheme.
Though they seem trivial, the colors assigned to each of the triangle mesh faces are used by Freesurfer to organize the anatomical labels assigned to every single point in the brain (i.e., every point assigned the same color is grouped in the same brain region). Freesurfer has tools (tksurfer) that allow you to go in and manually edit the parcellation if there is something ‘off’ about the label. For example, one of the sulci (the valleys in between the gyri) might extend too far up and over one of the adjacent gyri for your liking. Remember that Freesurfer uses computer algorithms that automate this parcellation. Though they do an extremely good job considering, there may be cases where your eye can improve upon the job that these algorithms have done. A tutorial on how to manually edit these parcellations using tksurfer can be found here. Aside from making minor fixes to the parcellations, you can use the procedure described in this tutorial to define anatomical regions of special interest to you, such as making a custom template that has definitions of the visual word form area or primary auditory cortex, based on some functional analyses you might have performed on some dataset.
Editing labels: simplified
1. Click around the region to make a loop that contains the region you want to extend (region A), and then region you want to extend it into (region B), like this.
2. Click "make closed loop" (underneath pial view), and click inside of the circle
Note: inside the circle should be two regions, region A and region B, do now, click one of these regions, it doesn't matter which
3. Open the "custom fill" dialogue.
4. Set fill conditions to "up to and including other paths."
5. Set fill from to "last clicked vertex."
6. Set action to remove from label (the correct region should already be selected in the action box)
7. Close custom fill dialogue box, click the other region inside the circle, and repeat steps 3-6. The circle should now be totally grey, indicating it doesn't have any labels.
8. Close custom fill dialogue. Click inside the enclosed region. This time, set the action to "add to existing label," and find the region you want to extend to in the drop down box (region A).
The enclosed region should now be filled with the label you wanted to extend. Select the path you worked on, select "remove path," and then unmark all vertices using the edit drop down.