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.
