The easiest thing to do is to specify your output of mri_surf2surf as mgh format instead of curv. The read that directly into matlab with our MRIread() matlab command (ie, no mris_convert stage). Make your computations in matlab, then write them out as mgh format using MRIwrite().

doug

Feng-Xian Yan wrote:

Hi,

  The mri_surf2surf command line was

mris_surf2surf --srcsubject xxx --sval xxx/surf/lh.thickness --sfmt curv --hemi lh --trgsubject fsaverage --tfmt curv --tval fsaverage/surf/lh.xxx.thickness

mris_convert –c fsaverage/surf/lh.xxx.thickness fsaverage/surf/lh.white fsaverage/surf/lh.xxx.thickness.asc

From these two command lines, I obtained the asc file with the coordinates of 163842 vertices and their thickness value.

Then, I did anova analysis to obtain F value and p value using MATLAB.

After I obtained the results from MATLAB, I want to map these results to inflated surface of fsaverage.

Could you tell me how to do and what command do I type? Or, you could recommend me another way to obtain the same map.

 
Thank you in advance!

 
Feng-Xian

2009/10/1 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>

   what was your mri_surf2surf command line?

   On Thu, 1 Oct 2009, Feng-Xian Yan wrote:

       Hi,

        But the number of vertex I obtain using mri_surf2surf is
       65536 each
       hemisphere. So, how can I do to make the number is closer to
       130,000?



       Thank you in advance!



       Feng-Xian


       2009/10/1 Bruce Fischl <fischl@nmr.mgh.harvard.edu

       <mailto:fischl@nmr.mgh.harvard.edu>>

           use mri_surf2surf. And you should have more than 65536
           vertices/hemisphere.
           Usually the # is closer to 130,000

           On Thu, 1 Oct 2009, Feng-Xian Yan wrote:

           Hi,


                I run all my subjects using recon-all ?subjid xxx
               ?autorecon-all. I get
               the cortical thickness value of each vertex (65536
               each hemisphere). Then
               I
               obtain F value and p value of anova analysis using
               MATLAB. Now, I want to
               map the results of anova to fsaverage. Could these
               values do that? Or, you
               could recommend me another way to obtain the same map.



               Thank you in advance!



               Feng-Xian




               2009/10/1 Bruce Fischl <fischl@nmr.mgh.harvard.edu

               <mailto:fischl@nmr.mgh.harvard.edu>>

               Hi Feng-Xian

                   have you run recon-all on your anatomical data?
                   What kind of data do you
                   want to map? Is it a functional volume?

                   cheers
                   Bruce

                   On Thu, 1 Oct 2009, Feng-Xian Yan wrote:

                   Hi,

                        I have a problem want to solve.
                       I want to map the data file (.xls or .txt) to
                       fsaverage. What command do
                       I
                       type?



                       Thank you in advance!


                       Feng-Xian

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