Lots of questions about lesions:
1) What is the best way to measure the size of a lesion in Freesurfer? Or should it be drawn in afni and transported to Freesurfer somehow?
2) What is the best way to measure how much of each ROI is affected by the lesion?
3) Line 25 lists "Left-lesion" and Line 57 lists "Right-lesion" in aseg.stats, but these are currently all zeros in brains that have clear lesions -- why? And why are those lines there if Freesurfer isn't recognizing a hole in the head as a lesion? Is there some option that must be selected to make this work?
4) Is it true that cortical lesions can throw off Freesurfer's ability to see landmarks, so that not only the lesion area might be mislabeled, but surrounding tissue and even distant tissue too? If so, is there a way around this problem built into Freesurfer? I have one brain with a large cortical lesion that looks like it parcellated okay, and another with a huge lesion that doesn't look right at all. Periventricular lesions look fine -- is this what others have found?
5) What is the best way to dump the parcellation data and the subcortical segmentation data back into afni (which files specifically) so that it can be viewed in 3D on the original structural brain as a mask?
Help would be much appreciated. Many thanks, Joan Fisher University of Chicago