Hi,
I’m not sure if you are running the chmod and the command separately or not.
You need two separate lines - the first is:
chmod 755 ec_plot.sh
and the second one is:
./ec_plot.sh myfile.ecclog
Try that and see if that fixes things.
If not then let me know more details about what “not running” means.
All the best,
Mark
> On 5 May 2019, at 17:00, Catherine Mewborn <[log in to unmask]> wrote:
>
> 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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