# ======================================================================
# ==                            video #1                              ==
# ======================================================================
cd
ls
afni_open afni_handouts/afni05_regression.pdf

cd AFNI_data6/afni
ls
afni

3dinfo epi_r1+orig

# ======================================================================
# ==                            video #2                              ==
# ======================================================================
3dinfo -VERB epi_r1+orig
# to exit "less", use 'q' to quit
3dinfo -VERB epi_r1+orig | less

cat rall_regress
3dinfo rall_vr+orig

cat stim_AV1_vis.txt
cat stim_AV2_aud.txt

3dDeconvolve -hweb


# ======================================================================
# ==                            video #3                              ==
# ======================================================================
cat rall_regress

# side task: add spaces after a backslash
afni_open -e rall_regress
file_tool -test -infile rall_regress
# and remove the bad spaces after the backslash so that file_tool is happy


cat rall_regress
3dinfo rall_vr+orig

afni_open -e motion.1D
1dplot -volreg -sepscl motion.1D &

cat stim_AV1_vis.txt
cat stim_AV2_aud.txt

timing_tool.py -hweb
timing_tool.py -help_basis

   # copy and paste the 3dDeconvolve and 1dplot commands
   # from the end of the "timing_tool.py -help_basis" output
   3dDeconvolve -nodata 200 0.1 -polort -1 -num_stimts 4      \
      -stim_times 1 '1D:0' GAM                                \
      -stim_times 2 '1D:0' 'WAV(1,1,3,8,0.2,2)'               \
      -stim_times 3 '1D:0' 'BLOCK(1)'                         \
      -stim_times 4 '1D:0' SPMG3                              \
      -x1D X.xmat.1D -x1D_stop
   1dplot -sepscl X.xmat.1D &

1dplot -volreg -sepscl motion.1D &

#       *** main 3dDeconvolve command ***
#           video #3 @ 30:35
tcsh rall_regress

ls -ltr
aiv rall_X.jpg
1dplot -sepscl rall_X.xmat.1D &
1dplot -volreg -sepscl motion.1D &


# ======================================================================
# ==                            video #4                      time 16:15
# ======================================================================

# review 3dDeconvolve output files and input files

# review files output from rall_regress
cat rall_regress

# finish and close handout

# view X-matrix, and also just the regressors of interest
1dplot -sepscl rall_X.xmat.1D &
1dplot -sepscl rall_X.xmat.1D'[6,7] &


# start viewing some results in afni

afni
# Underylay = epi_r1+orig
# open axial Image and Graph windows
# jump-to-ijk: 26 72 4

# now ponder the 3-run input (not just run 1)
# - same slice package
# - note command history
3dinfo rall_vr+orig


# in afni GUI: set Underlay to rall_vr
# graph window: 'm' down to a single voxel in graph matrix


# ======================================================================
# ==                            video #5                      time 39:33
# ======================================================================

# review regression results

# in afni GUI (with underlay rall_vr)
# jump-to-ijk: 26 72 4


# open 'New' (lower left corer) controller, B
# leave controller A windows on top, B windows on the bottom
# afni B: underlay = anat+orig, open all 3 Image windows

# note average time series value
#   afni A: Graph window -> right-click -> see Mean = 1284.764

# doubleplot: plot fit time series in same Graph window as rall_vr
# @ video time 3:20
# afni A: Graph -> Opt -> Tran 1D: None -> Dataset #N
#
# in Dataset #N plugin:
#   - toggle on Input #01
#   - Choose Dataset -> rall_fitts+orig -> Set
#   - Color : red -> dk-blue -> Set

# afni B: start explorig betas and t-stats
#   - Overlay = rall_func+orig

cat rall_regress
3dinfo -verb rall_func+orig

# afni B: choose color and threshold volumes
#   - OLay = V-A_GLT#0_Coef
#   - Thr  = V-A_GLT#0_Tstat
# note powers of 10 to scale threshold slider range
# threshold casually or with p-value
# afni B, above threshold slider bar ...
#   - on 'Thr' text, right-click -> set p=0.001
#   - crop image in coronal view, basically to zoom in
#   - play with crosshair colors
#   - Image window -> lower right corner 'c' to close xhairs

# review possible interpolation
# afni B: Define Datamode -> OLay Resam mode
#   - NN, Li, Cu or Bk

# underlay is at different resolution than overlay
#   - so must resample
#   - underlay = 0.9375 x 0.9375 x 1.0 mm^3
#   - overlay  = 2.75 x 2.75 x 3 mm^3
3dinfo rall_vr+orig
3dinfo anat+orig

# afni B: compare "jump-to-ijk 26 72 4" in underlay vs overlay

# cluster (@ 26:00)
# afni B: Clusterize
#   - can keep 2, 40, Bi-sided=Yes -> Set
#   - clear and reset to see speckles come and go
#   - Rpt (report button, under Clusterize)
#      - "Jump" to various clusters
#   - review auditory cluster (#6)
#   - note difference in fit peaks in rall_vr doubleplot