maxfilter_cenir -f run01.fif -st 20000 -corr 0.98 -bad 0221 0332 -trans meanmeanhp.fif -o run01_tsss.fif

#!/bin/bash

function display_usage() {
cat <<EOF

Usage:     $0 file1.fif file2.fif file3.fif ...
           $0 file1.fif file2.fif file3.fif ... -trans fileX.fif

This script takes any number of .fif files as input and generates up to three outputs per file.
For file1.fif:
    1/ a maxfiltered version file1_tsss.fif (using maxfilter -st)
    2/ a list of bad channels file1.bad (using xscan). If a file file1.bad already exists,
this step is skipped and the content of file1.bad will be used for step 3 below.
    3/ a maxfiltered version excluding these bad channels file1_tsss_nobad.fif (using maxfilter -bad )

If the -trans fileX.fif option is passed (often recommended), the head position in each file will be
set to that in fileX.fif

NOTE: this script will never overwrite any file. Remove previous versions of files if needed.

EOF
}

# first display usage if needed and parse trans arguments
if [ -z "$1" ]
then
    display_usage
    exit 1
else
    POSITIONAL=()
    while [[ $# -gt 0 ]]
    do
    key="$1"

    case $key in
        -trans)
        TRANS="$2"
        shift # past argument
        shift # past value
        ;;
        *)    # unknown option
        POSITIONAL+=("$1") # save it in an array for later
        shift # past argument
        ;;
    esac
    done
    set -- "${POSITIONAL[@]}" # restore positional parameters
    toprocess=$@
fi

# for each input file

for f in $toprocess
do
    dn=$(dirname "${f}")

    # make sure we use sss_config if next to the data
    if [ -d "${dn}/sss_config/" ]
    then
        xscan_cenir="xscan -ctc ${dn}/sss_config/ct_sparse.fif -cal ${dn}/sss_config/sss_cal.dat -st 20000 -corr 0.98 "
        maxfilter_cenir="maxfilter -ctc ${dn}/sss_config/ct_sparse.fif -cal ${dn}/sss_config/sss_cal.dat -st 20000 -corr 0.98 -trans $TRANS "
    else
        printf "Warning !\n No 'sss_config' directory next to the data in ${dn}\n\n maxfilter results may be inaccurate...\n\n"
        xscan_cenir="xscan -st 20000 -corr 0.98 "
        maxfilter_cenir="maxfilter -st 20000 -corr 0.98 -trans $TRANS "
    fi        
    
    # start 
    echo "processing $f"
    nf=`echo $f | sed -e 's/.fif$//g'`
    # if output _tsss file does not exist
    if [ ! -f ${nf}_tsss.fif ]
    then
        # run maxfilter -st
        echo "$maxfilter_cenir -f $f -o ${nf}_tsss.fif"
        $maxfilter_cenir -f $f -o ${nf}_tsss.fif
    else
        # if file exists, then skip
        echo "${nf}_tsss.fif exists. Skipping."
    fi
    
    # if a list of bad channels does not exist
    if [ ! -f ${nf}.bad ]
    then
        # create a list of bad channels        
        echo "detecting bad channels in $f"
        echo "$xscan_cenir -f $f"
        BAD_CHANNELS=`$xscan_cenir -f $f`
        echo $BAD_CHANNELS > ${nf}.bad
    else
        # else use existing list
        echo "${nf}.bad exists. Skipping automatic detection."
        BAD_CHANNELS=`cat ${nf}.bad`
    fi
    
    # if there is no bad channel
    if [[ -z "$BAD_CHANNELS" ]]
    then
        echo "No bad channels for $f"
    else
        # else create a _nobad.fif file where bad channels are excluded (interpolated)
        if [ ! -f ${nf}_tsss_nobad.fif ]
        then
            echo "Maxfilter ignoring bad channels..."
            echo "$maxfilter_cenir -f $f -o ${nf}_tsss_nobad.fif -bad $BAD_CHANNELS"
            $maxfilter_cenir -f $f -o ${nf}_tsss_nobad.fif -bad $BAD_CHANNELS
        else
            echo "${nf}_tsss_nobad.fif exists. Skipping."
        fi
    fi

done