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Dr. Jenkinson, 

I've been trying to extract motion data from some DTI files to analyze potential group differences in head motion. I ran across the script you created and the messages on the listserv from 2011 regarding this topic (see below). I copied the script into a txt file using notepad and tried to execute it using the command included in the message below (e.g., chmod 755 ec_plot.eh myfile.ecclog) but with no results. The script is not running or creating the new files as expected. I am not sure whether there is an issue with how I copied / saved the script or with the command I'm using to execute. Would greatly appreciate your help troubleshooting!

Best, 
Catherine Mewborn

On 11 January 2011 09:23, Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Charlotte,

I've previously written a little script to do this which I'm including below.
The displacements are always relative to the first timepoint (assuming the
reference_no of 0 was used in eddy_correct) but apart from that it is
pretty general.

If you run it you just need to give it the name of the .ecclog file (it also
assumes the original data has the same - without the .ecclog extension).
It will then produce ec_disp.png, ec_rot.png and ec_trans.png images
and the associated .txt files with the numbers in them.

Let me know if you have any trouble running it.
You should just need to copy the text below into a file (make sure you keep
it as pure text and don't use Word or anything like that to make the file)
called ec_plot.sh and then do :
 chmod 755 ec_plot.sh
If you put it in $FSLDIR/bin/ then it will be available wherever you are, but
if you put it somewhere else then you'll need to specify the path before
the "ec_plot.sh" name when you run it  (e.g.   ~/scripts/ec_plot.sh myfile.ecclog
if you put the file in ~/scripts/ )

All the best,
       Mark



#!/bin/sh

if [ $# -lt 1 ] ; then
 echo "Usage: `basename $0` <eddy current ecclog file>"
 exit 1;
fi

logfile=$1;
basenm=`basename $logfile .ecclog`;

nums=`grep -n 'Final' $logfile | sed 's/:.*//'`;

touch grot_ts.txt
touch grot.mat

firsttime=yes;
m=1;
for n in $nums ; do
   echo "Timepoint $m"
   n1=`echo $n + 1 | bc` ;
   n2=`echo $n + 5 | bc` ;
   sed -n  "$n1,${n2}p" $logfile > grot.mat ;
   if [ $firsttime = yes ] ; then firsttime=no; cp grot.mat grot.refmat ; cp grot.mat grot.oldmat ; fi
   absval=`$FSLDIR/bin/rmsdiff grot.mat grot.refmat $basenm`;
   relval=`$FSLDIR/bin/rmsdiff grot.mat grot.oldmat $basenm`;
   cp grot.mat grot.oldmat
   echo $absval $relval >> ec_disp.txt ;
   $FSLDIR/bin/avscale --allparams grot.mat $basenm | grep 'Rotation Angles' | sed 's/.* = //' >> ec_rot.txt ;
   $FSLDIR/bin/avscale --allparams grot.mat $basenm | grep 'Translations' | sed 's/.* = //' >> ec_trans.txt ;
   m=`echo $m + 1 | bc`;
done

echo "absolute" > grot_labels.txt
echo "relative" >> grot_labels.txt

$FSLDIR/bin/fsl_tsplot -i ec_disp.txt -t 'Eddy Current estimated mean displacement (mm)' -l grot_labels.txt -o ec_disp.png

echo "x" > grot_labels.txt
echo "y" >> grot_labels.txt
echo "z" >> grot_labels.txt

$FSLDIR/bin/fsl_tsplot -i ec_rot.txt -t 'Eddy Current estimated rotations (radians)' -l grot_labels.txt -o ec_rot.png
$FSLDIR/bin/fsl_tsplot -i ec_trans.txt -t 'Eddy Current estimated translations (mm)' -l grot_labels.txt -o ec_trans.png

# clean up temp files
/bin/rm grot_labels.txt grot.oldmat grot.refmat grot.mat

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