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-s)
   show all objects (All Objs button top of object controller)
   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 Max of range to 2
   play with slices - number of slices, planes, scroll
   change object to Anat+orig
   click v to volume render
   make anat transparent with Trn at 10
   switch back to func_slim
   move through slices some more (shift-scroll and sliders)
   turn off slices in func_slim
   click v to volume render


clusters in 3D
   3dClusterize -clust_nvox 200 -bisided -5 5 -ithr 2 -idat 1 -NN 1 \
        -inset func_slim+orig. -pref_map myclusters -overwrite
   3dZeropad -P 1 -prefix myclusters_zp -overwrite myclusters+orig
   IsoSurface -isorois+dsets -o clusttest.gii -overwrite -input myclusters_zp+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 5

   in suma, turn off convexity shading with 'b'
   show object controller (ctrl-s)
   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

   for specific regions,
   suma -onestate -i *Hippo*.gii -vol ~/abin/TT_N27+tlrc
   
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
   https://files.aievolution.com/hbm1801/abstracts/32549/2514_Glen.pdf
   curl https://files.aievolution.com/hbm1801/abstracts/32549/2514_Glen.pdf --output thickness.pdf
   evince thickness.pdf
   
Brain / brain region printing
   ConvertSurface -i TT_desai.Right-Hippocampus.k178.gii -o right_hippo.stl 

graymap carpet plots
   3dAutomask -prefix epi_r1_am epi_r1+orig
   3dGrayplot -mask epi_r1_am+orig. -input epi_r1+orig -prefix graymap
   3dGrayplot -mask epi_r1_am+orig. -input rall_vr+orig.'[0..148]' -overwrite -prefix graymap_vr
   aiv graymap*.png

SUMA balls
   https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/rois_corr_vis/suma_spheres.html
   https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/_downloads/demo_suma_spheres.tgz
   tar xzvf ~/Downloads/demo_suma_spheres.tgz
   suma -i surf_sphere.gii
   suma -i ico_combined.gii
   
Deface / Reface
   tcsh ~/afni_handouts/deface_anat.csh anat+orig anat+tlrc strip+orig
   suma -vol anat_deface+orig    (somewhat gory)
   @afni_refacer_run anat+orig.HEAD
   suma -vol anat.refacer.RESULT.nii
   suma -vol anat.refacer.RESULT.deface.nii (result with the -deface option, even gorier)

suma -dev clipping planes
   
DTI,Instacorr
   cd AFNI_demos/FATCAT_DEMO
   tcsh Do_00_PRESTO_ALL_RUNS.tcsh
   tcsh Do_09_VISdti_SUMA_visual_ex3.tcsh

Surface Instacorr
   cd ~/AFNI_data6/FT_analysis/FT.surf.results
   ./run_suma
   ctrl-s to open object controller
   Load Dset - errts
   Shift-D - to start Dot product correlation menu. Apply
   Shift-Ctrl-right click to set seed
   
Music and the Brain
   https://www.youtube.com/watch?v=7nS4u84ppf4

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