Dear Freesurfer experts,
I have tried to analyze with Freesurfer a dataset of images acquired with a 3D T1 sequence without inversion pulse (unfortunately, it is simply a FFE sequence and not a MP-RAGE). Contrast between grey and white matter is not optimal in this image, and when I run -autorecon2 step I obtain a very bad output (attached). "white/grey" surface seems to be where the pial surface is expected to be, and pial surface is in the middle of csf.
In your opinion, is it possible to obtain meaningful results with these images or not? Is there any setting of post-processing that I can change in order to obtain better surfaces?
Thank you for any suggestion
Kind regards,
Paola
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