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 template fromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplate
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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