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Hi,
I just wanted to say how impressed I am by the Freesurfer brain analysis software in general and to share some results of a comparison of the new *recon-all-clinical *option with various contrast types and resolutions.
This is only one subject, a healthy 62 year old male, so it's a very small study indeed, but the recon-all clinical does a great job in finding the correct volume of gray and white matter with some very low resolution clinical MRIs with non-ideal contrast MRI settings.
As you can see below, the T2 and T2 FLAIR gray and white volumes results with 0.72mm x 0.72mm x 6.5mm get very close to the correct volumes as measured by recon-all on the T1-MPRAGE scan. When I look at the actual detail of the slices it looks good too. Obviously it can't do magic and it has to basically "guess" where the information is completely missing when there is 6.5mm between slices.
The cortex tissue volumes for the T1 headscout, which is 1.6mm cubic voxels and has very low contrast between white and gray is also very good, considering the data it has to work with. The standard recon-all is not designed to work with a clinical T1 SE scan and naturally, does a much poorer GM/WM segmentation job.
Here are the results I got:
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So, well done to the whole Freesurfer crew and especially to the volunteers who devote so much time to this support list.
Michael McLaughlin, 2019 Parsons Medal Holder
