Hi Bruce, 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 from scratch(GW)( https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) 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 do the 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 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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