yes, the -w will create an optimal weighting to maximize gray/white contrast. The image it generates won't in general be physically realizable in an real MR acquisition. Not surprising that the tal stuff fails On Mon, 29 Apr 2013, Fred Dick wrote:
> Hi Bruce > > I'm using TR=20, flip=30, TE=5 - but possibly irrelevant as also have the -w > flag on. > > I originally thought this was from a bad brainmask, but then generated a good > one and same thing happening. > > > On 29 Apr 2013, at 14:27, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Fred >> >> we don't have much experience with this. Which synthesis are you using? You >> might need to use a different one for the talairaching to more closely match >> the atlas (maybe a TR=20,TE=2.5,flip=20-30 one) >> >> >> On Mon, 29 Apr 2013, Fred Dick wrote: >> >>> Dear all >>> >>> I'm having difficulties getting correct Talairach.lta's from synthetic >>> flash volumes (Bruce, you are probably sorry you ever told me about this!). >>> Basically the brain is over-scaled (bigger than it should be), which I >>> think is happening because the contrast is so good (gm much darker than wm). >>> >>> Is there an example of how to use the -flash_parms flag, and what >>> mri_em_register is expecting in the parameter file? >>> >>> Thanks, >>> >>> Fred >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> 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
