Dear Freesurfers,
I am just getting started using Freesurfer. I ran recon-all on my subjects for the first time and now would like to troubleshoot the output.
I watched the tutorial lectures and worked through the troubleshooting tutorial. Nevertheless, I am still uncertain which things I will have to correct (especially as editing too much and/or not to the same degree between subjects might do more harm than good).
Some errors are relatively obvious like the exclusion of white matter voxels from the white matter surface (see *1* on the screen shot of my own data)
I am far more uncertain about adding control points. For example, I do not know whether I should add those at the location denoted with *2* in my own data.
If so, there would be a lot of other, similar locations where I would add control points in my data. But this would also be true for the image used in the "Adding control points" tutorial. In the second screen shot, which displays this image, I have marked some locations where the white matter surface does not follow the one I would draw if I had to do it manually.
Is one supposed to correct all those imprecisions by adding control points?! What are the criteria for adding vs. not adding control points?
Thank you very much,
Janosch
