plot contour of functional ROIs in SUMA

AFNI Message Board
1

Hi AFNI and SUMA experts,

I’m trying to plot the contour of functional ROIs on inflated brain in SUMA and overlay with stat map. Can I ask what is best practice to do that?

Here is some context. For each subject there are one stat dataset for the main task and multiple mask datasets from functional localizer tasks.

Now I want to see how does the stat map for the main task overlapped with the ROIs returned by the functional localizers on inflated brain. Ideally, I would like the stat map shown in the SUMA as it is but mask dataset shown only the contour of the clusters. I found if I set the SUMA_ShowLabelDsetAtStartup to “Con” and it will nicely show contour of the ROIs in lh(rh).aparc.a2009s.annot.niml.dset and meanwhile I can still have stat map shown as overlay (which is the exact visualization I’m looking for). So I think if I somehow convert my mask dataset into the format like lh(rh).aparc.a2009s.annot.niml.dset it should work.

I also notice that @SUMA_Make_Spec_FS uses FSread_annot to generate the files needed, including the .niml.dset file I saw in the SUMA folder. But I’m not confident if I should go this route since it looks like I shouldn’t use FSread_annot out of the @SUMA_Make_Spec_FS. Can I ask what would be the steps you recommended?

Please let me know if you need more information.

Thanks very much!
Qianli

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3dVol2surf can generate the niml datasets to render in suma. There you can show contours and/or colors.

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Sorry for the delay! That’s the missing piece! Thanks very much!
Qianli