Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

Did you look in the summary file? If you have questions about that, can you send it? doug

On 06/11/2013 11:34 AM, Glen Lee wrote:

mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --sum sum.dat

On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

what is your full command line?


On 6/11/13 10:04 AM, Glen Lee wrote:

...

thanks Doug.
it worked and I got the following result on which I have
clarifying questions:

--------------
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0 1 81837  81837 <tel:1%20%C2%A0%2081837%20%C2%A081837>
----------------

1) I'm assuming that voxel here refers to vertex since I'm
submitting the surface data.

2) what does 'found 1 segmentations mean'?

3) the dimension is 81837mm^2, correct?




On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    It's --sum for this, not --o
    doug


    On 6/10/13 4:44 PM, Glen Lee wrote:

...

    Thanks Doug!

    I just tried, but I got an error:
    mri_segstats --seg mask.mgh --id 1 --i
    /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat
    ERROR: Option --o unknown

    I don't see --o option when I looked up mri_segstats --help
    either. FYI, I'm using v5.1.
    Any idea?



    On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>> wrote:


        Hi Glen, you can use

        mri_segstats --seg mask.mgh --id 1 --i
        $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat

        doug


        On 06/10/2013 03:17 PM, Glen Lee wrote:
        > Dear freesurfer users
        >
        > I'm wondering if there is any way of figuring out the
        surface size
        > within a mask image (mask.mgh)
        > which is generated after running a group-level GLM
        analysis (2nd RFX)
        > using mri_glmfit.
        >
        > As I'm thinking, this may be:
        >   number of vertex by dimension of one vertex (1mm).
        >
        > But I could be wrong and let me know if anyone knows
        the solution.
        >
        > -Glen
        >
        > fyi) the group analysis was performed in freesurfer
        sym space.
        >
        >
        >
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        --
        Douglas N. Greve, Ph.D.
        MGH-NMR Center
        greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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