Analyze MEG data and email when complete

run_tSSS.sh

#!/bin/sh

#
# The script should be run with the directory containing files to be analyzed.
# For each file in that directory, the script will run maxfilter with the
# parameters defined below, and save it to the output directory defined in
# SAVE_DIR. It will then email the address specified at the bottom
# (you@example.com) with the analysis log, containing the results of the
# analysis.
#

# Takes input argument of 
FILES=$1/*_[1-9].fif
# Set directory where output files will be saved
SAVE_DIR=/mnt/data/sinuhe/neuro-data/elli/tsssData

for f in $FILES
do
	fname=`basename $f | sed s/.fif//g`
	maxfilter \
		-f "$f" \
		-o $SAVE_DIR/$fname-tsss.fif \
		-origin fit \
		-frame head \
		-st 1 \
		-corr 0.980 \
		-waves $SAVE_DIR/$fname-tsssWaves.fif \
	| tee $SAVE_DIR/$fname-tsssLog.txt
	| mailx -s "$fname processing log" you@example.com
done