Monday, April 16, 2012

SUMA Demo

I've posted a demo of AFNI's surface mapper program, SUMA, over here on my screencast account. Specifically, I talk about how to map volumetric results generated in any fMRI software package (e.g., AFNI, FSL, SPM, BrainVoyager) onto a template surface provided by SUMA.

In this demo, I take second-level results generated in SPM and map them onto a template MNI surface, the N27 brain. All that is needed for doing this is a results dataset, a template underlay anatomical brain to visualize results on (here I use the MNI_caez_N27 brain provided in the AFNI binaries directory under ~/abin), and a folder called suma_mni that contains the .spec files for mapping onto the N27 brain. The suma_mni folder is available for download here. Just download it to the same directory, and you are good to go.

SPM 2nd-level results mapped onto template surface using AFNI / SUMA

I've outlined the steps in a word document, Volumetric_SUMA.docx, which is available at my website. Please send me any feedback if any of the steps are unclear.

Although this is an incredibly easy way to make great-looking figures, at the same time I would not recommend doing any ROI stats on the results mapped onto a surface using these steps. This is because it is essentially a rough interpolation of which voxel corresponds to which node; if you want to do surface ROI analyses, do all of your preprocessing and statistics on the surface (I may write up a demo of how to do this soon).

5 comments:

  1. kudos for the MNI-world SUMA interface. was looking for one for awhile

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  2. I'd be very careful in using the plugin in this way through the GUI. Use the 3dvol2surf utility that does the 'under the hood' work, and choose the adequate mapping function (max, avg etc'). There are many options to look at.

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    1. Thanks for the tip; I will look more into those options.

      -Andy

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  3. Hi,Andrew Thanks a lot, this is really helpful, the download link for .spec file is moved now, could you offered another spec download link, btw, I created spec file for freesurfer, but I don't know how to view it

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    1. Hey there, I've updated the link: http://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI_N27.tgz

      That should give you the files you need.

      -Andy

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