Wednesday, March 6, 2013

Surface Rendering in SPM

Because everybody loves a good surface rendering, SPM has a built-in, quick-and-dirty tool for splashing those results on your brain surface like splashing pool water at your friends while on your spring break trip to Cancun. (Swing and a miss - but hey, at least I went for it.) I think this technique is a little dated, and personally I think Freesurfer and SUMA do a much better job; but if you just want a quick figure, and if you want to at least earn the bare minimum of respect from your fellow researchers - classified as one step above slime and two steps below the macaque monkey - then this will help you earn that respect. I know what you're thinking: What about telling your fellow researchers that you dress yourself in the morning? Surprisingly, that doesn't work nearly as well.

More details on the strengths, limitations, and spraypaint-like features of surface rendering can be found in the following video.


8 comments:

  1. Hi Andy,
    I am wondering if it is possible to overlay two different results in same surface render in SPM.
    -Sabin

    ReplyDelete
    Replies
    1. Hi Sabin,

      For that, I would use MRIcron, which is a good way to overlay results onto a structural image or surface; I would start with that. I may do a series of tutorials on that soon...

      -Andy

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  2. Hi Andy i got one question, might be too simple

    I have a data set that constitutes voxel location in MNI space and corresponding activation in each location. I want to overlay those activation in MNI template image, I will be grateful if you suggest me some way to do it.
    Thanks

    ReplyDelete
    Replies
    1. Hi Ashok,

      This sounds like a typical parametric map; can you load it up through the Results tab in SPM? Once you do that and threshold it, you can click on "Overlays..." and select a template from the canonical directory in your SPM folder, e.g.:

      /Users/Andrew/spm12/canonical/single_subj_T1.nii

      Best,

      -Andy

      Delete
  3. Hello!

    I have 2 results: 1 for activations and 1 for deactivations. How can I put the 2 results on the same surface render in different colours?

    ReplyDelete
    Replies
    1. If you have two different colors, I would look into another rendering tool, such as MRIcron or SurfIce. I haven't found a way to do it through SPM's rendering tool.


      Best,

      -Andy

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    2. Thanks Andy! Do you know the optimal settings for mricron? The image that I created looks very odd in colour and orientation.

      Thanks.

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    3. Hmmm, I don't know of any optimal settings; you have to play around with those yourself. If I'm dealing with two contrasts, I usually plot one in green and one in red; any overlap will be shown in yellow, and I like the color scheme.


      Best,

      -Andy

      Delete