# Copy+pasteable commands from the AFNI Bootcamp's "afni11_roi.pdf"
# presentation

# Run these in this directory of AFNI Bootcamp data

  cd ~/AFNI_data6/afni

# modally smooth a dataset and have AFNI show that with discrete colors

  3dLocalstat -stat mode -nbhd 'SPHERE(-1.8)' -prefix myrois_mode1.8 myrois+orig.
  3drefit -cmap INT_CMAP -copytables myrois+orig myrois_mode1.8+orig

# Change grid/resolution of data set from (high res) anat to 
# (low res) EPI

  3dresample                   \
      -master rall_vr+orig     \
      -prefix anat_roi_resam   \
      -inset anat_roi+orig     \
      -rmode NN

# use ROI to mask to a dataset

  3dcalc -a rall_vr+orig. -b anat_roi_resam+orig \
          -expr 'a*step(b)' -prefix rall_masked

# Calculate average value per time point, dump to text file...

  3dmaskave                      \
      -mask anat_roi_resam+orig  \
      -quiet                     \
      rall_vr+orig > epi_avg.1D

# ... and view dumped text file results, using either of these

  more epi_avg.1D

# Dump *values* of a dset that are within a mask region into a 
# text file; no coordinate locations saved in this case, but could 
# save the coordinates of each voxel, too.

  3dmaskdump                                \
      -noijk                                \
      -mask anat_roi_resam+orig             \
      func_slim+orig'[2]' > Vrel-tstats.txt

# ... and view dumped text file results
 
  more Vrel-tstats.txt

# Compute separate statistics for each ROI in a volume

  3dROIstats                  \
      -mask 3rois+orig        \
      func_slim+orig'[0]'


# *** 3dClusterize example here with updated notation ***
# put the stats in a standard space for later use with whereami

  adwarp                       \
      -apar anat+tlrc          \
      -dpar func_slim+orig     \
      -dxyz 3

# Generate map of clusters

  3dClusterize -clust_nvox 200 -bisided -8.0 8.0 -ithr 2 -idat 1 -NN 1 \
    -inset func_slim+tlrc. -pref_map myclusters

# Find suprathreshold voxels, and make into clusters (kinda like GUI's
# Clusterize functionality and/or 3dclust)
 
  3dmerge                       \
      -prefix func_roi          \
      -dxyz=1                   \
      -1clip 99.0               \
      -1clust_order 1 200       \
      func_slim+orig.'[0]'


# ============ "Getting around with spheres" example ==========
# Try this:

adwarp                       \
    -apar anat+tlrc          \
    -dpar func_slim+orig     \
    -dxyz 3

# 1) In afni GUI, select:
#         Underlay -> anat, 
#         Overlay  -> func_slim
# 2) Switch 'view' to Talairach
# 3) Overlay index   -> vrel_coef,
#    Threshold index -> vrel_tstat
# 4) Clusterize (default opts OK), and Save Tabl
1dcat Clust_table.1D'[4..6]' > Clust_PeakXYZ.1D
3dUndump -srad 7.5 -master func_slim+tlrc -orient RAI   \
      -prefix clust_spheres -xyz Clust_PeakXYZ.1D