Re: [Freesurfer] Anatomical variation between individual surface and average template

You can just run mris_preproc --meas curv --o stack.mgh ... This will give you a stack from which you can compute the mean and stddev mri_concat stack.mgh --mean --o stack.mean.mgh mri_concat stack.mgh --std --o stack.std.mgh

doug

On 09/14/2012 01:55 PM, 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 mailto: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

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