# Copy+pasteable commands from the AFNI Bootcamp's "afni11_roi.pdf"
# presentation. 
#
# date = May 1, 2019


cd AFNI_data6/roi_demo

# 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


# 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
1dplot -yaxis 1000:1200:2:1 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]'


# Clusterizing example, using labels to specify stat and effect
# estimate volumes, and using p-value to specify voxelwise threshold.
3dClusterize                  \
   -1Dformat                  \
   -inset func_slim+orig      \
   -idat Vrel#0_Coef          \
   -ithr Vrel#0_Tstat         \
   -NN 2                      \
   -clust_nvox 200            \
   -bisided p=0.0001          \
   -pref_map Clust_map        \
   -pref_dat Clust_dat        \
   > Clust_report.1D

# ... and use the peak locations of clusters for identification in loaded
# atlases with 'whereami'
whereami                                  \
   -tab                                   \
   -coord_file Clust_report.1D'[1,2,3]'   \
   > Clust_whereami_peak.1D

# ... AND we could use the map of ROIs to find out locations, based on
# overlaps in loaded atlases, also with whereami
whereami                                  \
   -omask Clust_map+orig                  \
   > Clust_whereami_omask.1D


# 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 ==========

# This example shows how make spherical ROIs of a given radius around
# peak locations of clusters.

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) Set threshold value (say, p=0.001, or t-stat ~ 3))
# 5) 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