How does afni send output to suma? Trying to replicate with 3dVol2Surf

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1

I am trying to render cluster corrected, volumetric 3dttest++ results in surface space using 3dVol2Surf. Normally, I would simply use the afni and suma viewers together to accomplish this, but I need to use 3dVol2Surf since I would like to view multiple overlays in surface space.

For a quick test, I converted output from 3dClusterize (-pref_dat <some_map>) to surface space using 3dVol2Surf. I wanted to see if I could replicate what I would see if I used the normal afni - suma combo (combo A), but using 3dClusterize → 3dVol2Surf instead (combo B). Both gave quite similar outputs, but combo B gave small numbers of extraneous clusters I did not see in combo A.

I used the following 3dVol2Surf command, using the average map-function, with 10 steps and nodes as f_index:


for hemi in lh rh; do
    3dVol2Surf \
        -spec "suma_TT_N27/TT_N27_${hemi}.spec" \
        -sv "../suma_TT_N27/TT_N27_SurfVol.nii" \
        -grid_parent "${directory}/ispositive_${alphas[$t]}+tlrc" \
        -surf_A ${hemi}.smoothwm \
         -surf_B ${hemi}.pial \
         -map_fun ave \
        -f_step 10 \
        -f_index nodes \
        -out_niml  "${hemi}_clust.niml.dset \
        -overwrite
done

Is there an equivalent 3dVol2Surf command I could use to replicate what I see in combo A (i.e. afni <-> suma talking via niml)?

2

Hello,

Are you using the vol2surf plugin to afni?

Define Datamode → Plugins → Vol2Surf

If you actually turn that on (so it does not simply use a midpoint surface intersection) and set it up the way you would like to, it can output the corresponding 3dVol2Surf command.

  1. start the plugin, set up the options as you like, apply with “Set+Keep”
  2. in order to see a 3dVol2Surf command in the terminal window (where afni was launched), set the “debug level” to 2 or higher
  3. to see the effect of the options, cause afni to redisplay (e.g. press but do not move the Thresh slider in afni)

After step 3, the suma viewer should show the effects of the set options, and the (afni) terminal window should show the 3dVol2Surf command.

Does that seem reasonable?

  • rick
3

That did the trick. Thank you for your input!