AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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July 22, 2021 07:08PM
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)?
Subject Author Posted

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

ajschadler12 July 22, 2021 07:08PM

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

rick reynolds July 22, 2021 10:22PM

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

ajschadler12 July 23, 2021 05:23PM