Hi Yufeng

perhaps we should take a step back - what are you trying to achieve?

cheers Bruce On Tue, 18 Mar 2014, yufeng huang wrote:

Dear Bruce,  I am a new user of freesurfer. I just followed the process on the webside(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) to do the surface-based registration. However I do not to know what to do next after I get the lh.sphere.reg.newtemplate1 of each subjects. So could you please send me some papers about what to do next or some instruction about it.   I am confuse about what you mentioned(2. You can check the results by mapping the curvature of the subjects into the commmon space and seeing if they align (I think mri_surf2surf can be used for this). So if I can check the result by using tksurfer, However I do not know if the tksurfer will use the lh.sphere.reg.newtemplate1 instead of lh.sphere.reg. I am sorry that I can not find more information about the surface-based registration. I do not know how to check if the subject has already align to each other properly or not.      Thank you very much for you help! Please help me ASAP.    Yours Yufeng

2014-03-17 8:38 GMT-04:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: 1. Not if all you want to do is surface registration. If you want to do surface and volume you will need to do both.

  2. You can check the results by mapping the curvature of the
  subjects into the commmon space and seeing if they align (I
  think mri_surf2surf can be used for this).

  3. No, as recon-all won't use anything from your new coordinate
  system. It will only be useful for group analyses

  cheers
  Bruce


  On Sun, 16 Mar 2014, yufeng huang wrote:

        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. My question
        are as followed:
        1 I want to know if I need to use the
        mri_cvs_registrater to replace
        mri_register.
        2 I check the result and find it produce the
        lh.sphere.reg.newtemplate1 and
        rh.sphere.reg.newtemplate1 in each subjects's surf
        folder. I want to know
        how to check the result by using the new file.
        3 Should I need to re-run recon-all after the
        mri_register for every
        subjects?
        Thanks very much for your help!

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