Hi everybody.
I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions.
I have uploaded some images of the surfaces and segmentations of a subject to http://freesurfer.nikolasborrel.com, and my question is about the spikes in the inflated surfaces. I have selected two spikes on the surface (green mark), one for each hemisphere, and have found the corresponding location in tkmedit in each of the three directions (s,h,c).
For the spike in the left hemisphere (spike1_lh), I can't see what should be causing the spike. The segmentation looks correct.
For the spike in the right hemisphere (spike_rh), it seems like there are many 'isles of segmentations, but are these causing the spike? If yes, how should these isles be corrected?
Finally, how smooth is the inflated surface expected to be in a 'correct' case? Should a small amount of spikes be allowed, as long as they are not 'too severe'?
I can upload more images if needed, thanks in advance!
Kind regards Nikolas