#!/bin/tcsh


#===============================================================
# Start script from Parent directory,'Points'
# Verify that the script is being run from the proper directory:
#===============================================================

if ( ! -d Points ) then
    echo ""
    echo "error: this script must be run from the 'Points' directory"
    echo "exiting..."
    echo ""
    exit
endif

cd Points

#===============================================================
# Verify that the 'group_data' directory you're about to create 
# doesn't already exist:
#===============================================================

if ( -e group_data ) then
    echo "failure: the 'group_data' directory already exists"
    exit
endif

#===============================================================
# Begin by making a new directory called 'group_data'
#===============================================================

     mkdir group_data

#===============================================================
# cd into subject ED's directory
#===============================================================

     cd ED

#===============================================================
# make a copy of EDsprg+tlrc dataset.  Call it "sample_anat". 
# Move sample_anat+tlrc.*  into group_data directory
#===============================================================

     3dcopy  EDspgr+tlrc  sample_anat+tlrc
     mv sample_anat+tlrc.* ../group_data

#===============================================================
# cd out of ED's directory and up one level to parent directory 'Points'
#===============================================================

     cd ..

#===============================================================
# For each subject, copy their mean irf Talairached datasets into 'group_data'
# No need to use '3dcopy' b/c these are being moved to 'group_data' and 
# just being used for ANOVA. 
#=============================================================== 

     cp ??/??_??_irf_mean+tlrc.*  group_data

#===============================================================
# cd into 'group_data' directory and run ANOVA from there...
#===============================================================

     cd group_data

     3dANOVA2   -type 3 -alevels 4 -blevels 3 	\
		-dset 1 1  ED_TM_irf_mean+tlrc  \
		-dset 2 1  ED_HM_irf_mean+tlrc	\
		-dset 3 1  ED_TP_irf_mean+tlrc  \
		-dset 4 1  ED_HP_irf_mean+tlrc	\
		-dset 1 2  EE_TM_irf_mean+tlrc	\
		-dset 2 2  EE_HM_irf_mean+tlrc	\
		-dset 3 2  EE_TP_irf_mean+tlrc	\
		-dset 4 2  EE_HP_irf_mean+tlrc	\
		-dset 1 3  EF_TM_irf_mean+tlrc	\
		-dset 2 3  EF_HM_irf_mean+tlrc	\
		-dset 3 3  EF_TP_irf_mean+tlrc	\
		-dset 4 3  EF_HP_irf_mean+tlrc	\
		-amean 1 TM 			\
		-amean 2 HM 			\
		-amean 3 TP 			\
		-amean 4 HP  			\
		-acontr  1  1  1  1     AllAct 	\
		-acontr -1  1 -1  1 	HvsT 	\
		-acontr  1  1 -1 -1 	MvsP 	\
		-acontr  0  1  0 -1 	HMvsHP 	\
		-acontr  1  0 -1  0 	TMvsTP  \
		-acontr  0  0 -1  1 	HPvsTP 	\
		-acontr -1  1  0  0 	HMvsTM 	\
		-fa StimEffect 			\
		-bucket AvgANOVAv1

#===============================================================
# end of ht05_script2
#===============================================================