CPs are meant to correct failures due to bad tissue segmentation. Bad tissue segmentation usually take place when the contrast between the different brain compartments (i.e., grey [GM] and white matter [WM]) are unclear because of artifacts that are naturally present in the image.
That said, you can either find that some GM is left outside the pial boundary (red), or that some WM is erroneously considered as GM, and therefore, it is included within GM limits.
CPs, roughly, “pushes” the surface area (yellow), or the WM limits, so the pial will expand. So, if you happen to have GM misclassified as non-tissue, you can solve this with CPs. Likewise, if your GM limits are fine but WM is mistakenly assigned to the pial surface, you can also correct this with CPs.
Open the image:
tkmedit your_subject brainmask.mgz -aux T1.mgz -surfs
Scroll expecting not to spot any brighter or darker regions throughout the image. Remember that field inhomogeneities should have been already removed during the recon-all step.
Check that the boundaries between the pial (red) and the surface area (yellow) both follow a regular pattern. WM voxels normally have an intensity equal to or greater than 90, but lower than 110. GM voxels instead have an intensity below this threshold. It is wise to double-check what you think it is an error from different views (i.e., sagital, axial or coronal).
If you happen to find a voxel that it should be within the surface boundaries (1) press the “t” letter to enter in the voxel-edition mode and (2) click the mouse wheel to set a CP. Clicking the mouse’s right bottom will erase that CP you just have placed.
In the case you want to “push” the pial a little further, you can try to set the CPs right after the surface limits. Bear in mind that when you put a CP you are basically telling FS that you are 100% sure that such voxel is WM. Hence, FS will not only re-assign that voxel to WM but others with the same intensity. So, do not abuse of this feature. The lesser, the better.
Once you put the CPs that you consider necessary, click on File > Save control points and close tkmedit. Now, type the following in the Terminal:
recon-all -s <your_subject> -autorecon2-cp -autorecon3
Now, check the outcome of this and remember always backup your original data!