Hi list!
I was wondering what could cause this type of subcortical effect during FS preprocessing? I am referring to the white blank space where half the thalamus, part of the putamen, and all of the globus pallidus are not visable and Freesurfer just sort of "assumes" that they exist with its segmentation.
My theory is that the dimensions of the Nii file I am using are being stretched and it is causing this "assumption" of white space. My dimensions on this Nii files are X = 160 , Y = 240, and Z = 256. This would lead me to believe that the FSaverage brain that my nii is being warped to match has a greater x axis than my nii.
Is this correct? If so, is there any fsaverage options that has smaller dimensions? I assume this is an issue for analysis of subcortical measures, but should this effect cortical regions at all?
Hope you all are well and my message finds someone promptly, Jeffrey Crawford
