I'll look into it. I doubt it's been used for the previous scans. Given that, is there anything I can do (any flags/options to declare) that can deal with this kind of issue? I don't mind adding control points and whatnot, but an easy fix is obviously desirable.
Thanks, Chris ________________________________________ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Saturday, July 14, 2012 5:29 PM To: Watson, Christopher Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MPRAGE intensity variations Hi Chris Are you using prescan normalize? It helps a lot Cheers Bruce On Jul 13, 2012, at 1:00 PM, Chris Watson <christopher.wat...@childrens.harvard.edu<mailto:christopher.wat...@childrens.harvard.edu>> wrote: 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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
