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rej_MEEGArtReject.sh
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rej_MEEGArtReject.sh
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#!/bin/csh -f
#usage: MEEGArtReject.sh SubjType
#eg: ./MEEGArtReject.sh ac
#Computes the MEG and EEG channel rejections for all paradigms - 'ATLLoc' 'BaleenHP' 'BaleenLP' 'MaskedMM' 'AXCPT'- (only in the case of ya). This is computed after the eyeblink(HEOG/VEOG)Rejection.
echo 'CountEvents-CountBadChannels'
cd /autofs/cluster/kuperberg/SemPrMM/MEG/data/
foreach par ('BaleenHP' 'BaleenLP' 'ATLLoc' 'MaskedMM')
#foreach par ('BaleenHP' 'BaleenLP')
echo $par
foreach i (`cat /autofs/cluster/kuperberg/SemPrMM/MEG/scripts/function_inputs/$1.meg.all.txt`)
set subj = $1$i
echo $subj
rm /cluster/kuperberg/SemPrMM/MEG/data/$subj/ave_projon/logs/{$subj}_MEEGArtReject_{$par}
rm /cluster/kuperberg/SemPrMM/MEG/data/$subj/ave_projon/logs/{$subj}_MEEGArtReject-BadChan_{$par}
if ($par == 'ATLLoc') then
echo $par
if ( -e /autofs/cluster/kuperberg/SemPrMM/MEG/data/$subj/ave_projon/logs/{$subj}_ATLLoc-ave.log) then
cd /autofs/cluster/kuperberg/SemPrMM/MEG/data/$subj/ave_projon/logs/
foreach t ( {$subj}_ATLLoc-ave.log )
python /cluster/kuperberg/SemPrMM/MEG/scripts/rej_countBadChan.py $t $par
end
endif
else
echo $par
if (-e /autofs/cluster/kuperberg/SemPrMM/MEG/data/$subj/ave_projon/logs/{$subj}_{$par}Run1-ave.log ) then
cd /autofs/cluster/kuperberg/SemPrMM/MEG/data/$subj/ave_projon/logs/
foreach t ( {$subj}_{$par}Run?-ave.log )
python /cluster/kuperberg/SemPrMM/MEG/scripts/rej_countBadChan.py $t $par
end
endif
endif
cd ../../../
end
end
if ($1 == 'ya') then
echo 'AXCPT for ya'
foreach i (`cat /autofs/cluster/kuperberg/SemPrMM/MEG/scripts/function_inputs/$1.meg.all.txt`)
set subj = $1$i
cd /autofs/cluster/kuperberg/SemPrMM/MEG/data/$subj/ave_projon/logs
if (-e /autofs/cluster/kuperberg/SemPrMM/MEG/data/$subj/ave_projon/logs/{$subj}_AXCPTRun1-ave.log) then
foreach t ( {$subj}_AXCPTRun?-ave.log )
python /cluster/kuperberg/SemPrMM/MEG/scripts/rej_countBadChan.py $t AXCPT
end
endif
cd ../../..
end
endif
echo 'ComputeEvents'
cd /autofs/cluster/kuperberg/SemPrMM/MEG/data/
foreach par ('ATLLoc' 'BaleenHP' 'BaleenLP' 'MaskedMM')
#foreach par ('BaleenHP' 'BaleenLP')
echo $par
python /cluster/kuperberg/SemPrMM/MEG/scripts/rej_computeEvents.py $1 $par
end
echo 'Results saved in MEG/results/artifact_rejection/megeeg_rejection folder'