# ------------------------------------------------------------
# generate sine curves to show slice timing and correction
# (it is probably nice to run this in an empty directory)
#
# - 4 cycles across 20 time points -> 5 TRs per cycle
#     - simultaneous timing: -expr 'sin(2*pi*(4*l/20))'
#     - sequential timing:   -expr 'sin(2*pi*(4*(l+k/6)/20))'
# ------------------------------------------------------------

# create an empty 20x20x6 slice float image with 21 time points
nifti_tool                                                   \
    -infiles       MAKE_IM                                   \
    -prefix        d0.zero.nii -new_dims 5 20 20 6 1 21 0 0  \
    -new_datatype  16                                        \
    -mod_hdr                                                 \
    -mod_field     descrip 'for slice timing'

# --------------------------------------------------
# simultaneous timing
3dcalc -a d0.zero.nii -expr 'sin(2*pi*(4*l/20))' -prefix d1.simult.nii

# --------------------------------------------------
# interleaved timing (but slice n-1 needs to be fixed later)

# first: almost correct, but slice n-1 needs to be fixed
3dcalc -a d0.zero.nii -expr 'sin(2*pi*4*(l+mod(3*k,5)/6)/20)' -prefix d2.a.nii
# second: just for slice n-1
3dcalc -a d0.zero.nii -expr 'sin(2*pi*4*(l+5         /6)/20)' -prefix d2.b.nii

# combine: grab slice n-1 from the second dset, else from the first
3dcalc -a d2.a.nii -b d2.b.nii            \
       -expr 'a*step(5-k)+b*equals(k,5)'  \
       -prefix d3.inter.nii

# --------------------------------------------------
# add slice timing information to header
3dTcat -TR 2 -tpattern alt+z -prefix d4.as_acquired.nii d3.inter.nii
nifti_tool -rm_ext ALL -overwrite -infiles d4.as_acquired.nii

# --------------------------------------------------
# "correct" for the slice timing - to the start of the TR
3dTshift -quintic -tzero 0 -prefix d5.quintic.nii d4.as_acquired.nii
3dTshift -fourier -tzero 0 -prefix d5.fourier.nii d4.as_acquired.nii


### Apparently, 3dTcat can make a proper NIFTI header, but with a bad
#   AFNI header, and has the same problem directly making an AFNI dataset.
#   They differ in the 5th TAXIS_FLOATS entry, dz_sl.  So delete the AFNI
#   extension.
#               3dTcat.c: see if..TCAT_tpattern, or in general, set
#               dz_sl to dz (whyyyyy would they be different?)


# --------------------------------------------------
# make plots of: (xhairs at k=2, to leave k=0 at the bottom)
# (2 double plots means 2 controllers)
# - orig EPI:           d4.as_acquired.nii
# - orig+corrected:     d4.as_acquired.nii + d5.quintic.nii
# - simult+corrected:   d1.simult.nii      + d5.quintic.nii