#!/bin/tcsh
#
#       3ddeconvolution script 
#

if ($#argv <3) then
        echo "Usage: 3dDecSeed subjID [run name] [dir]  "
        exit 1
endif

set ptid = $1
set run = $2
set tdir = $3

cp ${run}wav ${tdir}

cd ${tdir}

foreach r (1 2 3 4)
set rn1 = `expr $r - 1`
rm ${ptid}${run}_${r}all.buc*.*
rm ${ptid}${run}_${r}_error*.*

3dDeconvolve \
-input ${ptid}${run}_alDBPM+tlrc \
-censor ${ptid}${run}TS_${r}_fullCensor.1D \
-polort 4 \
-num_stimts 7 \
-stim_file 1 ${ptid}${run}TS.1D'['${rn1}']' -stim_label 1 TS_$r \
-stim_file 2 ${ptid}${run}_tsh_vr_motion.1D'[0]' -stim_label 2 movRoll \
-stim_file 3 ${ptid}${run}_tsh_vr_motion.1D'[1]' -stim_label 3 movPitch \
-stim_file 4 ${ptid}${run}_tsh_vr_motion.1D'[2]' -stim_label 4 movYaw \
-stim_file 5 ${ptid}${run}_tsh_vr_motion.1D'[3]' -stim_label 5 movX \
-stim_file 6 ${ptid}${run}_tsh_vr_motion.1D'[4]' -stim_label 6 movY \
-stim_file 7 ${ptid}${run}_tsh_vr_motion.1D'[5]' -stim_label 7 movZ \
-errts ${ptid}${run}_${r}_error_ts \
-rout -bout -tout -nofull_first \
-bucket ${ptid}${run}_${r}all.buc


# StDev of error_ts (noise)
3dTstat -prefix ${ptid}${run}_${r}_err_ts_stdev -stdev -datum short ${ptid}${run}_${r}_error_ts+tlrc

# add noise to bucket, 3dd will calculate signal-to-noise
3dbucket -glueto ${ptid}${run}_${r}all.buc+tlrc \
-fbuc ${ptid}${run}_${r}_err_ts_stdev+tlrc

rm ${ptid}${run}_${r}_err_ts_stdev+tlrc*
rm ${ptid}${run}_${r}_error_ts+tlrc*

chmod a+x ${ptid}${run}_${r}all.REML_cmd 
./${ptid}${run}_${r}all.REML_cmd

end