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 > >
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