A guide to quantifying head motion in DTI studies

Monday, November 30, 2015 Do Tromp 3 Comments

"The widespread use of MRI has led to a wealth of structural and functional anatomical findings in patients with diverse psychiatric disorders that may represent insights into pathobiology. However, recent technical reports indicate that data from popular MRI research—particularly structural MRI, resting-state functional MRI, and diffusion tensor imaging—are highly sensitive to common artifacts (e.g., head motion and breathing effects) that may dominate the results. Because these and other important confounders of MRI data (e.g., smoking, body weight, metabolic variations, medical comorbidities, psychoactive drugs, alcohol use, mental state) tend to vary systematically between patient and control groups, the evidence that findings are neurobiologically meaningful is inconclusive and may represent artifacts or epiphenomena of uncertain value. The authors caution that uncritically accepting from study to study findings that may represent fallacies of all sorts carries the risk of misinforming practitioners and patients about biological abnormalities underlying psychiatric illness." - AJP 2015

echo ~~~Export displacement, rotation and translation for each subject~~~
for i in `ls *.ecclog`
do
prefix=`echo $i | awk 'BEGIN{FS=".ecclog"}{print $1}'`
ec_plot.sh ${i}
mv ec_disp.txt ${prefix}_ec_disp.txt
mv ec_disp.png ${prefix}_ec_disp.png
mv ec_rot.txt ${prefix}_ec_rot.txt
mv ec_rot.png ${prefix}_ec_rot.png
mv ec_trans.txt ${prefix}_ec_trans.txt
mv ec_trans.png ${prefix}_ec_trans.png
done

Echo ~~~Extract absolute translation average (mm) and euclidian distance~~~
for i in `ls *_ec_trans.txt`;
do
prefix=`echo $i | awk 'BEGIN{FS="_ec_trans"}{print $1}'`
count=`cat $i| wc |awk '{ print $1}'`
#Translation for x
x_total=`cat $i |tr -d - |awk '{s+=$1} END {print s}'`
x_average=`echo "scale=4; $x_total / $count" | bc`
#Translation for y
y_total=`cat $i |tr -d - |awk '{s+=$2} END {print s}'`
y_average=`echo "scale=4; $y_total / $count" | bc`
#Translation for z
z_total=`cat $i |tr -d - |awk '{s+=$3} END {print s}'`
z_average=`echo "scale=4; $z_total / $count" | bc`
#euclidian distance
euclidian=$(echo "scale=4;sqrt(($x_average*$x_average)+($y_average*$y_average)+($z_average*$z_average))" | bc)

echo ${prefix}, ${x_average}, ${y_average}, ${z_average}, ${euclidian} >> movement_data.txt
echo ${prefix}, ${x_average}, ${y_average}, ${z_average}, ${euclidian}
done