Andrew, Assuming it's a bash script, near the top, before it starts doing anything, add this line:
set -x Then re-run your script, redirecting the standard output and error to a file, e.g., script.log; then upload script.log here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi Donna On Sep 14, 2012, at 6:37 PM, Andrew Bock <[email protected]> wrote: > Thanks for the advice Tim, but I did paste these commands exactly as I have > them in my script (i.e. I don't use quotes). The quotes are only present in > the command line error. > > Oddly the other caret_command operation works (caret_command -file-convert), > it is only caret_command --surface-apply-transformation-matrix that results > in an error. Any other suggestions? > > Andrew > > On Fri, Sep 14, 2012 at 10:00 AM, <[email protected]> > wrote: > Send caret-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > > Today's Topics: > > 1. caret_command -surface-apply-transformation-matrix (Andrew Bock) > 2. Re: caret_command -surface-apply-transformation-matrix > (Timothy Coalson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Sep 2012 15:49:11 -0700 > From: Andrew Bock <[email protected]> > Subject: [caret-users] caret_command > -surface-apply-transformation-matrix > To: [email protected] > Message-ID: > <CAMaODrGEXAf4qLC_TKkC-XOKjb9ijK=xxzekj10ul4k-v8v...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I am attempting to follow the myelin maps pipeline outlined here: > http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps > > > >From my subjects directory I run the following commands: > > mri_convert -rl mri/rawavg.mgz mri/ribbon.mgz ribbon.nii.gz > > caret_command -file-convert -sc -is FSS surf/lh.white -os CARET > lh.white.coord.gii lh.white.topo.gii FIDUCIAL CLOSED -struct left > caret_command -file-convert -sc -is FSS surf/rh.white -os CARET > rh.white.coord.gii rh.white.topo.gii FIDUCIAL CLOSED -struct right > > caret_command -file-convert -sc -is FSS surf/lh.pial -os CARET > lh.pial.coord.gii lh.pial.topo.gii FIDUCIAL CLOSED -struct left > caret_command -file-convert -sc -is FSS surf/rh.pial -os CARET > rh.pial.coord.gii rh.pial.topo.gii FIDUCIAL CLOSED -struct right > > MatrixX=`mri_info mri/brain.finalsurfs.mgz | grep "c_r" | cut -d "=" -f 5 | > sed s/" "/""/g` > MatrixY=`mri_info mri/brain.finalsurfs.mgz | grep "c_a" | cut -d "=" -f 5 | > sed s/" "/""/g` > MatrixZ=`mri_info mri/brain.finalsurfs.mgz | grep "c_s" | cut -d "=" -f 5 | > sed s/" "/""/g` > Matrix1=`echo "1 0 0 ""$MatrixX"` > Matrix2=`echo "0 1 0 ""$MatrixY"` > Matrix3=`echo "0 0 1 ""$MatrixZ"` > Matrix4=`echo "0 0 0 1"` > Matrix=`echo "$Matrix1"" ""$Matrix2"" ""$Matrix3"" ""$Matrix4"` > > caret_command > -surface-apply-transformation-matrix lh.white.coord.gii lh.white.topo.gii > lh.white.coord.gii -matrix $Matrix > caret_command > -surface-apply-transformation-matrix rh.white.coord.gii rh.white.topo.gii > rh.white.coord.gii -matrix $Matrix > > caret_command > -surface-apply-transformation-matrix lh.pial.coord.gii lh.pial.topo.gii > lh.pial.coord.gii -matrix $Matrix > caret_command > -surface-apply-transformation-matrix rh.pial.coord.gii rh.pial.topo.gii > rh.pial.coord.gii -matrix $Matrix > > > Unfortunately I receive the following errors for the last 4 commands: > > ERROR: operation > "-surface-apply-transformation-matrix lh.white.coord.gii lh.white.topo.gii" > not found. > ERROR: operation > "-surface-apply-transformation-matrix rh.white.coord.gii rh.white.topo.gii" > not found. > ERROR: operation > "-surface-apply-transformation-matrix lh.pial.coord.gii lh.pial.topo.gii" > not found. > ERROR: operation > "-surface-apply-transformation-matrix rh.pial.coord.gii rh.pial.topo.gii" > not found. > > > Any help would be greatly appreciated. I am running Caret 5.65 on Linux64 > (Ubuntu). > > Andrew > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://brainvis.wustl.edu/pipermail/caret-users/attachments/20120913/4365833c/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 13 Sep 2012 20:55:03 -0500 > From: Timothy Coalson <[email protected]> > Subject: Re: [caret-users] caret_command > -surface-apply-transformation-matrix > To: "Caret, SureFit, and SuMS software users" > <[email protected]> > Message-ID: > <CAK_=tawC_PBsjz8--JOVLfK=kodf_jw5j3-n0egxq4vojhk...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Looks like a quoting problem to me. Your shell is interpreting > "-surface-apply-transformation-matrix lh.white.coord.gii lh.white.topo.gii" > as one argument, when it needs to be three. If these commands are run in a > script, quote each argument separately, rather than all together. If you > are pasting the commands exactly as you wrote them in the email, they > should work, unless your shell got messed up somehow (but since it didn't > include "-matrix" in the error message, I'm fairly sure it is quoting). > > Tim > > On Thu, Sep 13, 2012 at 5:49 PM, Andrew Bock <[email protected]> wrote: > > > Hello, > > > > I am attempting to follow the myelin maps pipeline outlined here: > > http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps > > > > > > From my subjects directory I run the following commands: > > > > mri_convert -rl mri/rawavg.mgz mri/ribbon.mgz ribbon.nii.gz > > > > caret_command -file-convert -sc -is FSS surf/lh.white -os CARET > > lh.white.coord.gii lh.white.topo.gii FIDUCIAL CLOSED -struct left > > caret_command -file-convert -sc -is FSS surf/rh.white -os CARET > > rh.white.coord.gii rh.white.topo.gii FIDUCIAL CLOSED -struct right > > > > caret_command -file-convert -sc -is FSS surf/lh.pial -os CARET > > lh.pial.coord.gii lh.pial.topo.gii FIDUCIAL CLOSED -struct left > > caret_command -file-convert -sc -is FSS surf/rh.pial -os CARET > > rh.pial.coord.gii rh.pial.topo.gii FIDUCIAL CLOSED -struct right > > > > MatrixX=`mri_info mri/brain.finalsurfs.mgz | grep "c_r" | cut -d "=" -f 5 > > | sed s/" "/""/g` > > MatrixY=`mri_info mri/brain.finalsurfs.mgz | grep "c_a" | cut -d "=" -f 5 > > | sed s/" "/""/g` > > MatrixZ=`mri_info mri/brain.finalsurfs.mgz | grep "c_s" | cut -d "=" -f 5 > > | sed s/" "/""/g` > > Matrix1=`echo "1 0 0 ""$MatrixX"` > > Matrix2=`echo "0 1 0 ""$MatrixY"` > > Matrix3=`echo "0 0 1 ""$MatrixZ"` > > Matrix4=`echo "0 0 0 1"` > > Matrix=`echo "$Matrix1"" ""$Matrix2"" ""$Matrix3"" ""$Matrix4"` > > > > caret_command > > -surface-apply-transformation-matrix lh.white.coord.gii lh.white.topo.gii > > lh.white.coord.gii -matrix $Matrix > > caret_command > > -surface-apply-transformation-matrix rh.white.coord.gii rh.white.topo.gii > > rh.white.coord.gii -matrix $Matrix > > > > caret_command > > -surface-apply-transformation-matrix lh.pial.coord.gii lh.pial.topo.gii > > lh.pial.coord.gii -matrix $Matrix > > caret_command > > -surface-apply-transformation-matrix rh.pial.coord.gii rh.pial.topo.gii > > rh.pial.coord.gii -matrix $Matrix > > > > > > Unfortunately I receive the following errors for the last 4 commands: > > > > ERROR: operation > > "-surface-apply-transformation-matrix lh.white.coord.gii lh.white.topo.gii" > > not found. > > ERROR: operation > > "-surface-apply-transformation-matrix rh.white.coord.gii rh.white.topo.gii" > > not found. > > ERROR: operation > > "-surface-apply-transformation-matrix lh.pial.coord.gii lh.pial.topo.gii" > > not found. > > ERROR: operation > > "-surface-apply-transformation-matrix rh.pial.coord.gii rh.pial.topo.gii" > > not found. > > > > > > Any help would be greatly appreciated. I am running Caret 5.65 on Linux64 > > (Ubuntu). > > > > Andrew > > > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://brainvis.wustl.edu/pipermail/caret-users/attachments/20120913/bf7153cb/attachment-0001.html > > ------------------------------ > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > End of caret-users Digest, Vol 108, Issue 1 > ******************************************* > > > > -- > Andrew Bock, Ph.D. > Department of Psychology > University of Washington > Seattle, WA 98195 > Tel: 206.543.3817 > Fax: 206.685.3157 > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
