Re: [Freesurfer] question about painting SPM results onto Freesurfer

Hi Doug,

As Bruce suggested, you may give me some help. My question is: I paint SPM results onto Freesurfer surface, is it possible to get the size and name of clusters on the surface?

Thanks

Karry

On Mon, Sep 3, 2012 at 10:16 PM, keepmoon keepmoon1224@googlemail.comwrote:

Hi Bruce,

Thanks for your answer! Yes. I would like to know the size of the cluster after painting on the surface.

Expecting Doug's reply!

Thanks in advance!

Karry

On Mon, Sep 3, 2012 at 7:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

you mean the size of the cluster on the surface? Yes, you can do that, but you'll need to wait for Doug's return for the details

cheers Bruce

On Mon, 3 Sep 2012, keepmoon wrote:

Hi Bruce,

...

Thanks for your detailed explaination! I have one more question about it! Is it possible to get cluster size for being painted SPM results on freesure surface (like getting the cluster size of cortical thickness in QDEC )? Is there any command getting it?

Any idea will be appreciated! Thanks! Karry

On Mon, Sep 3, 2012 at 5:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu

...

wrote: Hi Karry

  painting is done by mri_vol2surf and you can use it to specify
  how you want the sampling to be done. We typically sample the
  volume halfway our from the gray/white boundary, or sometimes a
  bit lower to avoid vascular artifacts at the pial surface. That
  said, it is quite flexible and you can use it to sample however
  you wish (e.g. average over the bottom third of cortex,
  etc....). When we sample we don't inspect the value, just grab
  it from the volume and assign it to the surface so if there are
  significant cluster that aren't intersected by the sampling band
  you specify they will not appear on the surface.

  cheers
  Bruce

  On Sun, 2 Sep 2012, keepmoon wrote:

        Hello everyone,

        I just read the information about "paintig SPM
        results onto Freesurfer"
        (http://surfer.nmr.mgh.**harvard.edu/fswiki/SpmPainting<http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting>

**). It shows how to painting SPM results from statistic step (ex. spmT.img) to surface space. I tested the procedure and it worked. But I don't understand what is displayed on Freesurfer surface. Are all the significant differences from SPM statistic results are displayed on this surface? or some part of t values are displayed (which part)? As cortical thickness displayed on surface, each thickness value is painted on each vertex. But here t-value image from SPM is volume image, how to paint it on surface?

        Someone could give a little detailed explaination??

        Thanks in advance

        Karry

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