Aha, I shall quickly try with the non -w weighting and see what happens. Thanks! On 29 Apr 2013, at 15:05, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> 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
