#!/bin/tcsh

               Unix help

# -------------------------------------------------------------------
# if the afni directory is already here, whine a bit and terminate the script

if ( -e ARzs_data/afni ) then
    echo ""
    echo "Failure:"
    echo ""
    echo "The resulting afni directory already exists.  Please move the"
    echo "afni directory and then re-run the script.  Example:"
    echo ""
    echo "    mv ARzs_data/afni ARzs_data/afni.bak"
    echo ""

    exit
endif

               Unix help



# -------------------------------------------------------------------
# start in the top level data directory

cd ARzs_data

               Unix help

# -----------------------------------------------------------------------------
# create AFNI dataset from spgr I-files - will move them to afni dir later

to3d -prefix ARzs_spgr -spgr SPGR_data/I.*

               AFNI howto  Unix help  'to3d -help'

# -----------------------------------------------------------------------------
# create AFNI datasets from both EPI runs

cd EPI_data

               Unix help

Ifile -nt '???/I.*'

               AFNI howto  Unix help  'Ifile -help'

# change the prefix for the output file in GERT_Reco

sed 's/OutBrick/ARzs_EPI/' GERT_Reco > new_GERT_Reco

               Unix help

# now run the new_GERT_Reco script

tcsh new_GERT_Reco

               AFNI howto   Unix help

# -------------------------
# store outliers in a subdir

cd afni
mkdir outliers
mv ARzs_EPI*Outliers.1D outliers
cd ..

               Unix help

# -------------------------

# put the new afni directory back at the top level

mv afni ..

               AFNI howto  Unix help

# go back to top level data directory

cd ..

               Unix help

# -----------------------------------------------------------------------------
# put our spgr anat dataset into that new afni directory

mv ARzs_spgr+orig.* afni

               Unix help

# -----------------------------------------------------------------------------
# do volume registering

cd afni

3dvolreg -prefix ARzs_EPI_r1_vr -base ARzs_EPI_r2+orig'[155]' ARzs_EPI_r1+orig
3dvolreg -prefix ARzs_EPI_r2_vr -base ARzs_EPI_r2+orig'[155]' ARzs_EPI_r2+orig

               AFNI howto  Unix help  '3dvolreg -help'

# average the two volume registered time series datasets

3dcalc -a ARzs_EPI_r1_vr+orig -b ARzs_EPI_r2_vr+orig \
	-expr '(a+b)/2' -prefix ARzs_EPI_avg 

               AFNI howto  Unix help  '3dcalc -help'

# -----------------------------------------------------------------------------
# create 1D file (Ref_ARzs.1D) containing ideal reference function

waver	-GAM -dt 2 -numout 160		\
	-inline	15@0			\
		15@1 7@0 15@1 8@0	\
		15@1 7@0 15@1 8@0	\
		15@1 7@0 15@1 8@0	\
		10@0			\
	> Ref_ARzs.1D

               AFNI howto  Unix help  'waver -help'

# gasp! actual statistical analysis of data! ...

3ddelay -input ARzs_EPI_avg+orig -ideal_file Ref_ARzs.1D -fs 0.5 -T 45

               AFNI howto  Unix help  '3ddelay -help'

# -----------------------------------------------------------------------------
# extra stuff

3dIntracranial -anat ARzs_spgr+orig -prefix ARzs_spgr_NoSkl

               AFNI howto  Unix help  '3dIntracranial -help'

echo "results are left in directory: ARzs_data/afni"

               Unix help