Re: [Freesurfer] what is the minimum information needed to create a custom template?

I see. Usually we start with a sphere, and create a sphere.reg for a bunch of subjects, then remake the template with those Bruce On Tue, 3 Sep 2013, David Romano wrote:

Hi Bruce,

The workflow that I mentioned from the wiki is for creating a new template in the absence of any ?.sphere.reg files;  here's relevant language from the webpage:

---

"Creating a registration template from scratch (GW)

(This section reports on what I (GW) have learned of the registration process from Bruce Fischl. and Doug Greve, along with reading the source code. I have not actually tried it.)

The process of creating a template involves calculating a "mean" (across subjects) pattern of curvature-related values, along with the variance of these variables. This task is performed by program mris_make_template. However, mris_make_template expects the input subjects to be already aligned (ie: already have ?h.sphere.reg files). This of course will not be the case if you are about to create a template!"

---

This is context for my question.

Thanks, David

On Tue, Sep 3, 2013 at 3:50 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi David

  usually you need a ?h.sphere.reg as the ?h.sphere files are in
  (arbitrary) spherical coordinates, while the ?h.sphere.reg ones
  are in registered ones

  cheers
  Bruce

  On Tue, 3 Sep 2013, David Romano wrote:

        Hi everyone,

        If I only have lh.sphere and lh.sulc files for each
        of collection of
        subjects, would this be enough information to
        generate a template for
        registering further subjects?  

        I was thinking of trying to follow the workflow
        described on the page:

             
        https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates

        (in the section titled "Creating a registration
        template from scratch
        (GW)"), but wasn't sure whether more than just
        native spherical coordinates
        and convexity information would be implicitly
        required by the
        mris_make_template command. (The "Positional
        Arguments" table that appears
        on the page:

            
        https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_template

        only asks explicitly for references to the
        hemisphere data for a collection
        of subjects.)

        Thanks in advance for you help,
        David Romano

        (P.S.  There's also appers to be a typo in the
        "Positional Arguments" table
        I mentioned above:  In the description section for
        position 2, the {hemi}
        and {sphere_name} values seem to be reversed.)

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