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
