On 04/05/2014 09:49 PM, ye tian wrote:

Dear Bruce and Doug,

Would you please shine some light on what the freesurfer files mean?

For example, rh.orig, once mris_converted, starts with

115750 231496
21.097221 -65.951393 -18.834326 0
20.621031 -66.165680 -18.995041 0
.....

I thought that this file gives all unidentified regions, since 0=unknown, but it doesn't make sense.

Furthermore,
1) What do the first two numbers mean?

I think the first is the number of vertices and the 2nd the number of faces

2) Not all files can be fed into mris_convert. Do you recommend using read_surf.m instead?

Thank you very much!

Sincerely,
Ye

On Tue, Mar 4, 2014 at 7:30 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:

    Hi Ye

    it is both that, and volumes of label indices (e.g. 17=Left
    Hippocampus) and surface models (triangles, edges, points) and
    scalar and vector fields over them.

    cheers
    Bruce



    On Mon, 3 Mar 2014, ye tian wrote:

        Dear Bruce and Doug,
        Thank you very much!

        Would you please tell me more about what "freesurfer data"
        actually is? Is
        it composed of pixel positions and intensities? If that's the
        case, how do
        you calculate cortical thickness?

        Thank you very much!

        Sincerely,
        Ye




        On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve

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

        wrote:

              Can you be more specific about what you mean by "freesurfer
              data"? Each
              subject has 300MB of "data"
              doug

              On 02/27/2014 10:48 PM, ye tian wrote:
              > Dear Freesurfers,
              >
              > I would like to do some customized model fitting for
        cortical
              > thickness. Is there a way to export freesurfer data
        into R or
              simply
              > as a text?
              >
              > Thank you very much!
              >
              > Sincerely,
              > Ye
              >
              >
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        --
        Douglas N. Greve, Ph.D.
        MGH-NMR Center

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