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
