I have been working with Freesurfer running reconstructions on Mp2rage MRI data for an internship, and while I think I have been able to figure out how to correctly skullstrip the noisy Mp2Rage image, the professor I am doing the internship with has said that the aseg and aparc results of the reconstruction are not totally accurate. I'm not sure why, although I suspect it's because the skullstrip still has some noise around the edges. I'm going to try brainvoyager or premade matlab scripts to denoise the mp2rage image rather than doing it manually by multiplying the mask generated for the skullstrip of the inversion pulse with the original image.
However, even if I figure out this issue I will still need a way to check my results. I am able to tell that the major structures of the brain are in the right place, but the professor told me this is not enough to verify that the reconstruction is an accurate representation of the original MRI data (which makes sense). I don't know how he's able to tell that the reconstruction is inaccurate by looking at the segmentation, but he wants me to actually run some type of analysis to figure out how to check the data rather than asking him.
He is being intentionally vague because he wants me to figure out how to do this without his help, but I am pretty stuck. He mentioned something about statistical analysis, but it wasn't clear what he meant. I am looking for any tips to mathematically verify that the reconstructions are accurate, and also possibly ways to fix inaccuracies that aren't too extreme.
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source https://www.reddit.com/r/Radiology/comments/u6jn15/how_to_verify_accuracy_of_freesurfer_cortical/
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