Hi Janosch
it's impossible to tell from a single slice whether those points should
be added or not. The white matter in your image is *very* dark in these
regions, do you know why? To decide whether to add them or not you should
check a couple of slices in each direction (or look in multiple
orientations) to make sure that the white matter is actually dark and it's
not partial volume effects. The approach I would take is iterative - add a
couple then rerun up to the first inflation and see if things have been
improved significantly. This is fast, maybe 5-10 minutes, not sure. You
shouldn't need to add a ton. Even one control point in the middle of a dark
region can have a large effect.
cheers
Bruce
On Thu, 30 Jan 2014, Janosch Linkersdörfer wrote:
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
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