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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Hi David

I would do what I suggested:

1. Create a template froma ?h.sphere. 2. Register a bunch of subjects to the template to create a bunch of shpere.reg files. 3. Rebuild the template from the sphere.reg files. 4. Register to this one 5. Rebuild the template

cheers Bruce

On Tue, 3 Sep 2013, David Romano wrote:

Suppose the subjects were from a species of primate that has never been scanned before, and that native spheres have been found for each subject -- how would you create a sphere.reg for a bunch of subjects in that case?   From the webpage I mentioned, it seems that it suggests repeated applications of mris_make_template to increasingly large subsets of the original collection, but I can't tell from the webpage or the wiki for mris_make_template whether more than just native spheres and convexity information are needed.   Does the approach you refer to need any more than that?

Thanks, David

On Tue, Sep 3, 2013 at 4:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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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        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
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