show volume in space
  - could have surfaces from freesurfer
  anat, strip datasets - multiple slices, rendering
  func_slim - range, threshold  

   cd AFNI_data6/afni
   suma -vol anat+orig -vol func_slim+orig
   open object controller (ctrl-n)
   show all objects
   change to func_slim volume
   change I (Intensity) volume to Vrel#0_Coef. T (Threshold) to Vrel#0_Tstat
   change Cmp (color map) to bgyr19
   change threshold to 7.0
   change object to Anat+orig
   change Max to 2
   click v to volume render
   make anat transparent with Trn at 10
   switch back to func_slim
   move through slices (shift-scroll and sliders)
   turn off slices in func_slim
   click v to volume render


clusters in 3D
   IsoSurface -isorois+dsets -o clusttest.gii -input Clust_mask+orig
   afni -niml
   suma -onestate -i *.gii -vol strip+orig. -sv anat+orig

   in afni, set overlay to Vrel#0_Coef and threshold to Vrel#0_Tstat
   threshold around 4

   in suma, turn off convexity shading with 'b'
   show object controller (ctrl-n)
   show all objects
   select strip+orig
   change number of axial slices to 5:20
   right-click on slices, scroll with shift-scroll or arrow
   change transparency of strip+orig slices with ctrl-o or trn button
   change transparency of all other objects with 'o' key
   change points mode of individual regions with 'p' key
   talk to afni with 't'
   (even more advanced, use Vol2Surf plugin with map all, normals, norm len=-4)

show atlas in suma
   mkdir atlassurfs
   cd atlassurfs
   IsoSurface -isorois+dsets -o TT_desai.gii -input ~/abin/TT_desai_dd_mpm+tlrc.

   suma -onestate -i *.gii -vol ~/abin/TT_N27+tlrc.

   opacity, points -hiding mesh, some or all - exploring and limiting

show atlas with volume
  slices, rendered volume
   afni -niml anat+tlrc  ~/abin/TT_desai_dd_mpm+tlrc.
   change overlay to TT_desai_dd_mpm+tlrc
   suma -vol anat+tlrc -vol ~/abin/TT_desai_dd_mpm+tlrc.
   Press 't' in suma to talk to afni
   turn on volume rendering for anat+tlrc
   click 's' in volume rendering control to turn off selection and allow click through to atlas   


Thickness - methods - examples, comparison with FreeSurfer

merged atlas rois

connectivity - connections?

Claustrum/roi extract - display a particular region
        
suma -dev clipping planes

Brain printing

graymap carpet plots

Acknowledgements in suma
   https://afni.nimh.nih.gov/afni/community/board/read.php?1,146293,146293
   http://afni.nimh.nih.gov/sscc/staff/glend/collaborations/NIMLcontributors.tgz
   suma -gdset /home/dglen/macaque_connections/contributor_connections.niml.dset