Oops i just realized I only sent this to Bruce:

Thanks!  It looks like this involves some manual intervention.  Matt., I assume you're not manually making control points on 1000s of subjects (I imagine this is for the human connectcome project).  Is your code public somewhere?

Cheers,

Michael

On Tue, May 15, 2012 at 7:36 PM, Michael Waskom <mwaskom@stanford.edu> wrote:

Thanks!  It looks like this involves some manual intervention.  Matt., I assume you're not manually making control points on 1000s of subjects (I imagine this is for the human connectcome project).  Is your code public somewhere?

Cheers,

Michael

On Tue, May 15, 2012 at 9:14 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

sure, here's mine. Matt's is probably a lot more polished as they intend to run it on hundreds or thousands of subjects

On Tue, 15 May 2012, Michael Waskom wrote:

Hi Bruce,
Sounds cool, I'd be very interested in checking out the script.

Cheers,
Michael

On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
     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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