More details on the strengths, limitations, and spraypaint-like features of surface rendering can be found in the following video.
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.
More details on the strengths, limitations, and spraypaint-like features of surface rendering can be found in the following video.
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Hi Andy,
ReplyDeleteI am wondering if it is possible to overlay two different results in same surface render in SPM.
-Sabin
Hi Sabin,
DeleteFor 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
Hi Andy i got one question, might be too simple
ReplyDeleteI 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
Hi Ashok,
DeleteThis 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
Hello!
ReplyDeleteI 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?
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.
DeleteBest,
-Andy
Thanks Andy! Do you know the optimal settings for mricron? The image that I created looks very odd in colour and orientation.
DeleteThanks.
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.
DeleteBest,
-Andy