Hi Yufeng

can you remember to cc the list? And yes, if all you want is a common surface-based coordinate system for your subjects then there is no need for you to run mris_register yourself - it is done by recon-all. All you need to do is run mri_vol2surf for each individual, then map the resulting overlays to fsaverage with mri_surf2surf

cheers
Bruce


On Wed, 19 Mar 2014, yufeng huang wrote:

Hi Bruce,
What does" rerun the registration - just use the ?h.sphere.reg files." mean?
Just using noting or using as follow  code to produce new
?h.sphere.reg.newtemplate?

mris_register -curv surf/lh.sphere \
     $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
     surf/lh.sphere.reg.newtemplate


2014-03-19 10:42 GMT-04:00 yufeng huang <trista.yfh@gmail.com>:

      I want to do is map all the individual activation maps into a
      common surface-based coordinate system. So I do not need to

      follow the process of creating a registration template fromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplate

      s) to do the surface-based registration.
  1If I just use the ?h.sphere.reg which produce by recon-all. But I
want to know : Who is the average subject at this time. The fsaverage?
  2 So at this time all I need to do is using mri_surf2surf onto
fsaverage surface? Or I should using mri_vol2surf first and do the
mri_surf2surf next?
Thanks very much!



2014-03-19 9:46 GMT-04:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      Hi Yufeng

      if all you want to do is map all the individual activation
      maps into a common surface-based coordinate system,then
      there is no need to create your own atlas and rerun the
      registration - just use the ?h.sphere.reg files.


      If there is some other reason you want to create your own
      template/atlas, then you can check the results by using
      make_average_subject to create a new version of
      fsavverage, and mapping each subject's curvature file into
      your new coordinate system using mri_surf2surf onto that
      average subject's surface. Then see if they align. You
      don't need to do anything about the inflated or other
      surfaces. Use mri_vol2surf to map the data onto each
      individual subject's surface, then mri_surf2surf with your
      new registration file to map it to your new average
      subject.

      cheers
      Bruce


      On Wed, 19 Mar 2014, yufeng huang wrote:

            Dear Burce,
               I have 20 normal subjects, and I want to do
            inter-subject surface-based
            registration to all of them. So each one's
            surface can align properly to the
            other subject’s surface. After that I can put
            the functional data onto the
            surface which has aligned to each other
            already.
              And now I followed the process of creating a

            registration templatefromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemp
            late

            s) to do the surface-based registration. 
            Round 1, all reference subjects
            data are registered to the initial template,
            producing ?h.sphere.myreg0.
            (I've coordinated the suffix numbers with the
            template used to produce the
            registration.) Using that registration, a new
            template (mytemp1.tif) is made
            using all reference subjects as input. Round 2
            is essentially a repeat of
            Round 1, but produces an improved template
            (mytemp2.tif) because Round 2's
            initial registration step is based on a better
            template than in Round 1.
              I get the lh.sphere.reg.newtemplate1 and
            rh.sphere.reg.newtemplate1 in
            each subjects's surf folder. I do not know how
            to check the result about if
            every subject has aligned to each other
            properly. And I do not know what
            should I do next.
              My question is :
            1 How can I check about the result as if every
            one has aligned each other
            properly?
            2 And what should I do next, I can not know if
            the functional data can
            aligned to the new surface properly. If I can
            use mri_surf2surf or
            mri_vol2surf can be used for this.
            3 The lh.sphere.reg.newtemplate1 and
            rh.sphere.reg.newtemplate1is just for
            sphere, and  how about the inflate aligned  to
            each other?
               Yours Yufeng




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