Hello,
I ran a subject through recon-all both with and without the "-mprage" flag, and naturally got different results. I'm attaching a screenshot of the pial and main surfaces, along with the orig.mgz of the same slice. The image tends to be brighter in the frontal lobe, and there is an intensity change when going through the slices. The scanner is Siemens 3T (Trio, I think), using a 32-channel head coil. The imaging parameters are: (not sure which are most relevant)

TR: 1410
TI: 800
TE: 2.2
Matrix: 256x256
FOV: 256
Flip angle: 9 deg
ImagingFrequency: 123.259181
Pixel bandwidth: 199

Is there anything I can do to improve the results?
Thanks,
Chris

PS When I didn't use the '-mprage' flag, I used the '-nuintensitycor-3T' flag. So I changed 2 separate things.

<orig.png>

<subj_mprage_flag.png>

<subj_no-mprage_flag.png>

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