#pre-step for later... cd ~/AFNI_demos/FATCAT_DEMO tcsh Do_00_PRESTO_ALL_RUNS.tcsh afni_proc.py QC if you haven't seen it yet! @DriveAfni plugout_drive README.driver (@DriveSuma, DriveSuma) @chauffeur_afni @chauffeur_afni \ -ulay anat+orig \ -prefix PRETTY_PICTURE \ -montx 5 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 3 \ -do_clean aiv PRETTY_PICTURE.*.png ***** 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 cd ~/AFNI_data6/afni 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 n27_ml_surfs cd n27_ml_surfs IsoSurface -isorois+dsets -input ~/abin/MNI_caez_ml_18+tlrc -o ml.gii opacity, points -hiding mesh, some or all - exploring and limiting for specific regions, suma -vol ~/abin/MNI_caez_N27+tlrc. -onestate -i ml.*_Thalamus.*.gii ***** Thickness - methods - examples, comparison with FreeSurfer https://afni.nimh.nih.gov/pub/dist/HBM2018/OHBM_2018_Thickness.pdf curl https://afni.nimh.nih.gov/pub/dist/HBM2018/OHBM_2018_Thickness.pdf --output thickness.pdf afni_open thickness.pdf # this example uses FT SUMA data cd ~/AFNI_data6/FT_analysis/FT/SUMA # combine ribbons (left=1, right=2), no overlap 3dcalc -a lh.ribbon.nii.gz -b rh.ribbon.nii.gz -expr 'a+2*step(b)' \ -prefix bothribbons.nii.gz # compute depth as distance transform 3dDepthMap -prefix corticaldepth.nii.gz -zeros_are_zero \ -input bothribbons.nii.gz # depth map can be shown as volume with smoothwm or any surface or volume suma -vol bothribbons.nii.gz -vol corticaldepth.nii.gz -i std.141.lh.smoothwm.gii # project to volume (for demo, just left hemisphere) 3dVol2Surf -spec std.141.FT_both.spec \ -surf_A std.141.lh.pial.gii -surf_B std.141.lh.smoothwm.gii \ -map_func max -grid_parent corticaldepth.nii.gz -f_steps 10 \ -out_niml corticaldepth.lh.niml.dset -sv FT_SurfVol.nii # double the maximum depth to approximate thickness 3dcalc -a corticaldepth.lh.niml.dset -expr 'a*2' -prefix corticalthick.lh.niml.dset # smooth the data on the surface SurfSmooth -spec std.141.FT_both.spec -surf_A std.141.lh.smoothwm.gii \ -met HEAT_07 -input corticalthick.lh.niml.dset \ -output corticalthick_smooth.lh.niml.dset -fwhm 8 # show just the left hemisphere for quicker viewing suma -spec std.141.FT_lh.spec -sv FT_SurfVol.nii -input corticalthick_smooth.lh.niml.dset & # set range from 2-5 # compare to FreeSurfer **** leading "edge" research cd ~/AFNI_data6/afni 3dedgedog -automask -input anat+orig. -prefix edgedog afni 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 curl -O https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/_downloads/demo_suma_spheres.tgz tar xzvf ~/Downloads/demo_suma_spheres.tgz cd ~/demo_suma_spheres suma -i surf_sphere.gii suma -i ico_combined.gii suma -gdset graph_set_sphere.niml.dset **** Deface / Reface # if already run, @afni_refacer_run, skip to suma views below cd ~/AFNI_data6/afni @afni_refacer_run -input anat+orig.HEAD -mode_all -prefix dereface suma -vol dereface.deface.nii.gz suma -vol dereface.reface.nii.gz ***** layer FMRI + clipping planes cd @Install_SURFLAYERS_DEMO1 cd ~/SURFLAYERS_DEMO1 tcsh s05_afni_sl_demo_V1_calcarine # clipping planes DTI,Instacorr # if already started above, skip to Do_09... cd AFNI_demos/FATCAT_DEMO tcsh Do_00_PRESTO_ALL_RUNS.tcsh # run this for visualization tcsh Do_09_VISdti_SUMA_visual_ex3.tcsh Surface Instacorr tcsh s03.ap.surface tcsh -xef proc.FT.surf 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 Acknowledgments 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