Hi Bruce and Michael, That would be very nice. Do I just email you the hi-res *whole-brain*mprages, or is their another way to get the images to you?
On the other hand, I'm a fair hand at scripting. I'd be willing to experiment with any scripts that you might provide. Last, and on an unrelated note. Is that programming position at Freesurfer still open? I know someone looking for an interesting and challenging position like that. Best, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Tue, May 15, 2012 at 6:00 AM, Matt Glasser <m...@ma-tea.com> wrote: > Yes, I have a modified script working. For the white surface, the > essentials are the same as Bruce's script but it has some additional stuff > (e.g register T2w to T1w), and I call it in the middle of the recon-all > rather than at the end. For the pial surface, I have done some more > complicated stuff, which I'd love to talk to Bruce about some more some > time. :) > > Peace, > > Matt. > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, May 15, 2012 7:29 AM > To: Michael Waskom > Cc: FreeSurfer > Subject: Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future > > you need to call mris_make_surfaces directly. It's a bit complicated as you > need to intensity normalize and register the hires volume to the surfaces > first. I have an example script if anyone is interested, but no one has > used it yet but me I don't think (unless Matt Glasser has gotten his > version working, which on second thought he probably has) > > On Mon, 14 > May 2012, Michael Waskom wrote: > > > Hi Bruce, > > Is there a flag for this on recon-all? Or do you need to use > > mri_make_surfaces directly? > > > > Best, > > Michael > > > > On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > > wrote: > > Hi Joshua > > > > yes, we already have upgraded mris_make_surfaces to take higher > > res data > > and refine the surfaces with it. Haven't tried it on the aseg > > yet, but if > > you upload a sample dataset I could see how hard it is. > > > > cheers > > Bruce > > On Mon, 14 May 2012, > > Joshua Lee wrote: > > > > > Dear Freesurfers, > > > > > > Over the last years, MR imaging technology hasimproved such > > that sub 1-mm > > > isotropic scans can be obtained with good signal to noise > > characteristics. > > > For example, our lab uses 0.7mm isotropic structural MR > > images. I understand > > > that the Freesurfer pipeline will up-sample these to 1mm > > isotropic, but it > > > seems a shame that so much information is left unused which > > could be used to > > > improve the accuracy of sub-cortical and cortical > > segmentation. My question > > > is whether there are any plans at Freesurfer to change the > > reference > > > standard resolution from 1mm isotropic, or provide another > > solution that can > > > help researchers make the most of your technology. > > > > > > Sincerely, > > > > > > > > > Joshua > > > - > > > Joshua > > > > > > > > > > > _______________________________________________ > > 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 >
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