MEG_scripts/makeSTC.sh at master · KuperbergLab/MEG_scripts · GitHub

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#!/bin/csh -f

#usage makeSTC.sh subjID exp logfile
#you need to change the exp variable and condList below to run STCs for your experiment of interest

set exp = $2
echo $exp

if ( $exp == "MaskedMM_All" ) then
	set condList = ( 4 2 3 )
	echo $condList
endif

if ( $exp == "BaleenLP_All" ) then
	set condList = ( 3 5 )
	echo $condList
endif

if ( $exp == "BaleenHP_All" ) then
	set condList = ( 5 7 9 10)
	echo $condList
endif

if ( $exp == "AXCPT_All" ) then
	set condList = ( 1 2 3 4 5 6 )
	echo $condList
endif

if ( $exp == "AXCPT-equalisedTar_All" ) then
	set condList = ( 1 2 3 4 )
	echo $condList
endif

if ( $exp == "AXCPT-equalisedPri_All" ) then
	set condList = ( 1 2 )
	echo $condList
endif


####################################

if ( $#argv == 0 ) then
    echo "NO SUBJECT ARGUMENT"
    exit 1
endif

if ( $#argv == 1 ) then
    set log='./makeSTC.log'
    echo "Logging to default log..." >>& $log
endif

if ( $#argv == 2 ) then
    set log='./makeSTC.log'
    echo "Logging to default log..." >>& $log
endif

if ( $#argv == 3) then
    set log=$3
endif

# if log exists, delete
if ( -e $log ) then
    rm $log
endif

###################################

setenv SUBJECT $1
cd /cluster/kuperberg/SemPrMM/MEG/data/$1/ave_projon

mkdir stc
mkdir stc/$exp

foreach c ($condList)

# 	echo Unmorphed mne >>& $log
# 	mne_make_movie --inv $1_$exp-ave-7-meg-inv.fif --meas $1_{$exp}-ave.fif --set $c --bmin -100 --bmax -.01 --stc stc/$exp/$1_{$exp}_c{$c}-mne.stc --smooth 7 >>& $log
#
# 	echo Unmorphed spm >>& $log
# 	mne_make_movie --inv $1_$exp-ave-7-meg-inv.fif --meas $1_{$exp}-ave.fif --set $c --bmin -100 --bmax -.01 --stc stc/$exp/$1_{$exp}_c{$c}-spm.stc --smooth 7 --spm >>& $log
#
# 	echo Unmorphed sLORETA >>& $log
# 	mne_make_movie --inv $1_$exp-ave-7-meg-inv.fif --meas $1_{$exp}-ave.fif --set $c --bmin -100 --bmax -.01 --stc stc/$exp/$1_{$exp}_c{$c}-sLORETA.stc --smooth 7 --sLORETA >>& $log
#
	echo Morphed mne >>& $log
 	mne_make_movie --inv $1_$exp-ave-7-meg-inv.fif --meas $1_{$exp}-ave.fif --set $c --bmin -100 --bmax -.01 --stc stc/$exp/$1_{$exp}_c{$c}M-mne.stc --smooth 7 --morph fsaverage >>& $log

	echo Morphed spm >>& $log
	mne_make_movie --inv $1_$exp-ave-7-meg-inv.fif --meas $1_{$exp}-ave.fif --set $c --bmin -100 --bmax -.01 --stc stc/$exp/$1_{$exp}_c{$c}M-spm.stc --smooth 7 --spm --morph fsaverage >>& $log

 	echo Morphed sLORETA >>& $log
	mne_make_movie --inv $1_$exp-ave-7-meg-inv.fif --meas $1_{$exp}-ave.fif --set $c --bmin -100 --bmax -.01 --stc stc/$exp/$1_{$exp}_c{$c}M-sLORETA.stc --smooth 7 --sLORETA --morph fsaverage >>& $log

# 	echo Morphed spm >> & $log
# 	mkdir stc/$exp-megeeg
# 	mne_make_movie --inv $1_$exp-ave-7-meg-eeg-inv.fif --meas $1_{$exp}-ave.fif --set $c --bmin -100 --bmax -.01 --stc stc/$exp-megeeg/$1_{$exp}-megeeg_c{$c}M-spm.stc --smooth 7 --spm --morph fsaverage >>& $log

end

########FIX GROUP ON ALL FILES########
chgrp -R lingua .