Thanks Bruce. one more question:

This is my command (5 subjects)

mris_make_template lh sphere.reg subj1 subj2 subj3 subj4 subj5 ./Temp5subj.tif

where I select sphere.reg as sphere surface. I assume 1) that the generated template Temp5subj.tif is in the Freesurfer buckner40 spherical space and 2) the mean and variance of the measure included in the new template are also in the buckner40 spherical space. Is that correct? 

In addition, could you simply explain what's the difference between lh.curv and lh.sulc. Both files look similar and include negative and positive valude, except that lh.sulc seems to be smoothed. Thanks.

Best,
Liang

2012/9/14 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
yes, you can use mris_make_template to generate these results (it's what we used to create the tif files in the first place)

On Fri, 14 Sep 2012, liang wang wrote:

Dear Bruce,
Thanks for pointing me those information. That .tif file includes the mean and
variance for the population sample that was used in Freesurfer. I would like to get
similar measures for our own subjects. I think I could use the surface file (like
surf/?h.sulc) in each subject folder to compute the mean and variance, right? Is
this file already in spherical template space? Thanks again.

Best,
Liang

2012/9/14 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
      Hi Liang

      yes, that information is encoded in the .tif file that is the target of
      the registration. You can use mrisp_paint to copy a frame out of
      $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif

      the tif file is 3 sets of triplets in different frames. The first is
      the mean of the measure, the second is the variance and the third is
      the degrees of freedom. The 3 triplets are for the curvature of the
      inflated surface, the sulc and mean curvature of the white surface.

      cheers
      Bruce

      On Thu, 13 Sep 2012, liang wang wrote:

            Dear FS folkers,
            I am working on a functional probabilistic atlas. I find
            that some functional
            regions (particular along a big sulcus) show quite high
            probability value over a
            large sample, whereas the probability for some regions are
            quite lower. I think
            this disparity could be accounted for by the anatomical
            variation on each surface
            node that appears while surface-based
            registering individual surface to the average
            template that was provided by Freesurfer. For instance, the
            anatomical variation
             could be pretty small within a big sulcus (like central
            sulcus). 

            I assume that Freesurfer output a file which characterizes
            this type of anatomical
            variation. Could someone point me which file it is and how
            to use it to create a
            group-level measure in order to clear display somewhere has
            large variation.
            Thanks.

            Best,
            Liang

            --
            Liang Wang, PhD
            Neuroscience of Attention and Perception Laboratory
            Princeton Neuroscience Institute
            Princeton University
            Princeton, NJ, 08540






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--
Liang Wang, PhD
Neuroscience of Attention and Perception Laboratory
Princeton Neuroscience Institute
Princeton University
Princeton, NJ, 08540






--
Liang Wang, PhD
Neuroscience of Attention and Perception Laboratory
Princeton Neuroscience Institute
Princeton University
Princeton, NJ, 08540