Hi Paola, that looks pretty bad. What version are you running? You can try using rhe expert opts to set the g/w intensities, or drop the dataset on our site and we'll take a look. cheers Bruce
On Tue, 28 Dec 2010, Paola Valsasina wrote:
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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