Did you paste the command into the script from somewhere? I'm thinking maybe the whitespace in those places isn't a simple space, and it is confusing the shell, but if you typed it in manually, that shouldn't happen...perhaps you could upload the script itself to the place donna suggested?
Tim On Fri, Sep 14, 2012 at 6:37 PM, Andrew Bock <ab...@u.washington.edu> 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, > <caret-users-requ...@brainvis.wustl.edu>wrote: > >> Send caret-users mailing list submissions to >> caret-users@brainvis.wustl.edu >> >> 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 >> caret-users-requ...@brainvis.wustl.edu >> >> You can reach the person managing the list at >> caret-users-ow...@brainvis.wustl.edu >> >> 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 <ab...@u.washington.edu> >> Subject: [caret-users] caret_command >> -surface-apply-transformation-matrix >> To: caret-users@brainvis.wustl.edu >> 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 <tsc...@mst.edu> >> Subject: Re: [caret-users] caret_command >> -surface-apply-transformation-matrix >> To: "Caret, SureFit, and SuMS software users" >> <caret-users@brainvis.wustl.edu> >> 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 <ab...@u.washington.edu> >> 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 >> > caret-users@brainvis.wustl.edu >> > 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 >> caret-users@brainvis.wustl.edu >> 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 > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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