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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 fischl@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 > > >
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