Saturday, September 8, 2012

Mapping Results onto SUMA (Part 2)

In a previous post I outlined how to overlay results generated by SPM or FSL onto a SUMA surface and published a tutorial video on my Techsmith account. However, as I am consolidating all of my tutorials onto Youtube, this video has been uploaded to Youtube instead.

There are few differences between this tutorial and the previous one; however, it is worth reemphasizing that, as the results have been interpolated onto another surface, one should not perform statistical analyses on these surface maps - use them for visualization purposes only. The correct approach for surface-based analyses is to perform all of your preprocessing and statistics on the surface itself, a procedure which will later be discussed in greater detail.

A couple of other notes:

1) Use the '.' and ',' keys to toggle between views such as pial, white matter, and inflated surfaces. These buttons were not discussed in the video.

2) I recommend using SPM to generate cluster-corrected images before overlaying these onto SUMA. That way, you won't have to mess with the threshold slider in order to guess which t-value cutoff to use.

More AFNI to come in the near future!


7 comments:

  1. I think you just saved my life! Thank you. This is so helpful!

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    1. Hey Mark, glad to hear it! We aim to please.

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  2. Hi Andrew - Any idea where you can download different surfaces to map results onto? I used the link in your youtube post but it seems to only give slightly inflated versions of the brain (not the full inflation you had in your video example) - or maybe I'm doing something wrong? Thanks for all of this, saved my life as well! (https://www.youtube.com/redirect?q=http%3A%2F%2Fafni.nimh.nih.gov%2Fsscc%2Fstaff%2Fziad%2FMisc_Download%2Fsuma_mni.tgz&redir_token=vWlgrjesprV6643enDida1rFo3V8MTQxMjc4NDQ3MEAxNDEyNjk4MDcw)

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    1. Hey there,

      That link may be a little old, and they may be using something new. However, I think it should still work. Have you tried using the '.' and ',' keys to toggle between different views? That might help.

      -Andy

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  3. Hi Andrew,

    Do you know if there is anyway I can export the overlay out in the form of "value-at-each-surface-vertex"? Ideally in the same format as the surface file used in Freesurfer?

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    1. Hey there,

      I haven't done that, but you should look into 3dVol2Surf and Freesurfer's mri_convert. Those are my best guesses.

      -Andy

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    2. 3dVol2Surf works great, thanks for the tip

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