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.
recon-all -autorecon3 -subjid FS_202
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
To see an idealized brain for reference, open a new terminal and leave SUBJECTS_DIR as the freesurfer subjects folder. Then run tksurfer fsaverage -annot aparc lh pial. There are several "fsaverage" brains, so feel free to try out different ideal brains, but they should all be similar. Remember that not all brains will look the same, so the parcellations will likely differ from the ideal version, but it can at least be used as a reference for tricky regions.
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. If the "make closed loop" option is causing the terminal to lag, just cancel it via ctrl+c, reclick around the region, and make the closed loop again. Unmark all vertices.
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. Click on the section you want to remove (and fill in with another label). 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, and click ok.
7. Close custom fill dialogue box. The region you wanted to remove should be grey, indicating it no longer has a label.
8. Close custom fill dialogue. Click inside the enclosed region. This time, set the fill conditions to both "up to and including other paths" and "up to and including other labels." Set 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."
BE SURE TO SAVE AFTER EACH EDIT. The editing process for autorecon3 is very easy to accidentally mess up, and there is no undo for these label edits! Saving often will prevent loss of data. To do so, make sure to export annotation, don't just "save surface." You will export to either lh.annot.aparc or rh.annot.aparc depending on which hemi you are editing. Be sure to save to the correct hemisphere!