Dear caret users, I am following the 'FS-to-F99 tutorial' and managed to process the right hemisphere so that it appears like Figure 10, and Left hemisphere until 3.4.
I am now facing a problem at 3.6 where the superimposed individual and atlas coordinates appear in completely different positions. The script outcome seems ok and ends without error (see below). If I next run Stage-3.FS-toF99.sh the atlas and deformed individual landmarks appear completely distorted and I obtain the following outcome from the script (see below). Any help would be greatly appreciated Thank you and have a nice day Julia bash-3.2$ '/Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/ Stage-2B.FS-to-F99.sh' + . Params.FS-to-F99.txt ++ set -x ++ TUTORIAL=no ++ CASE=120810MILO ++ HEMISPHERE=left ++ VOXDIM=0.5 ++ ATLAS_DIR=/Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET ++ CARET_DIR=/Freiwald/lab_files/opt/caret/ ++ SPECIES=Macaque ++ NUMBER_NODES=78317 + cp Params.FS-to-F99.txt /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/ + export SUBJECTS_DIR=/Freiwald/jsliwa/cooked/anatomicals/ + SUBJECTS_DIR=/Freiwald/jsliwa/cooked/anatomicals/ ++ cut -c1 ++ echo left ++ tr '[:lower:]' '[:upper:]' + HEM_FLAG=L ++ echo left ++ cut -c1 + FS_HEM_PREFIX=lh + FS_HEM_PREFIX=/Freiwald/jsliwa/cooked/anatomicals//120810MILO/surf/lh + '[' L = L ']' + MATRIX='-1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0' + caret_command -surface-apply-transformation-matrix /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/Macaque.ATLAS.sphere.6.74k.coord /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/Macaque.sphere_6.RIGHT_HEM.74k.topo /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/Macaque.sphere_6.RIGHT_HEM.X-Flip.74k.coord -matrix -1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 + caret_command -surface-border-unprojection /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/Macaque.sphere_6.RIGHT_HEM.X-Flip.74k.coord /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/Macaque.sphere_6.RIGHT_HEM.74k.topo /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/Macaque.F99.R.LANDMARKS.Reg-with-120810MILO.L.74k_f99.borderproj Macaque.F99.LANDMARKS-for-120810MILO.L.SPHERE.X-Flip.border + caret_command -surface-border-projection 120810MILO.L.SPHERICAL_STD.78317.coord 120810MILO.L.CLOSED.78317.topo Macaque.F99.LANDMARKS-for-120810MILO.L.SPHERE.X-Flip.border Macaque.F99.LANDMARKS-for-120810MILO.L.78317.borderproj + '[' no = yes ']' + sed /SPHERICALcoord_file/d 120810MILO.L.Stage-2.spec + mv 120810MILO.L.Stage-2.spec.rev 120810MILO.L.Stage-2.spec + echo SPHERICALcoord_file 120810MILO.L.SPHERICAL_STD.78317.coord + echo borderproj_file Macaque.F99.LANDMARKS-for-120810MILO.L.78317.borderproj + caret_command -scene-create 120810MILO.L.Stage-2.spec 120810MILO.L.Stage-2.scene 120810MILO.L.Stage-2.scene '3. Compare 120810MILO.L with F99 landmarks' -surface-overlay UNDERLAY SURFACE_SHAPE 'Folding (120810MILO.L) Smooth_MW' -1 -show-borders -window-surface-types WINDOW_MAIN 520 500 SPHERICAL CLOSED LATERAL -window-surface-types WINDOW_2 520 500 SPHERICAL CLOSED MEDIAL + . Params.FS-to-F99.txt ++ set -x ++ TUTORIAL=no ++ CASE=120810MILO ++ HEMISPHERE=left ++ VOXDIM=0.5 ++ ATLAS_DIR=/Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET ++ CARET_DIR=/Freiwald/lab_files/opt/caret/ ++ SPECIES=Macaque ++ NUMBER_NODES=78317 + cp Params.FS-to-F99.txt /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/ + export SUBJECTS_DIR=/Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99 + SUBJECTS_DIR=/Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99 + cat ++ echo left ++ cut -c1 ++ tr '[:lower:]' '[:upper:]' + HEM_FLAG=L ++ echo left ++ cut -c1 + FS_HEM_PREFIX=lh + FS_HEM_PREFIX=/Freiwald/jsliwa/cooked/anatomicals/120810MILO/surf/lh + INCLUDE_FUNCTIONAL_MAP=no + sed ' s#SPECIES#Macaque#g s#HEMISPHERE#left#g s#CASE#120810MILO#g s#space UNKNOWN#space #g ' /tmp/header.7870.txt + echo CLOSEDtopo_file 120810MILO.L.CLOSED.78317.topo + echo FIDUCIALcoord_file 120810MILO.L.Midthickness_MWS.78317.coord + echo INFLATEDcoord_file 120810MILO.L.INFLATED.78317.coord + echo SPHERICALcoord_file 120810MILO.L.SPHERICAL_STD.78317.coord + echo borderproj_file 120810MILO.L.LANDMARKS.78317.borderproj + echo surface_shape_file 120810MILO.L.78317.surface_shape + echo area_color_file 120810MILO.L.AREAS.areacolor + echo border_color_file Macaque.LANDMARKS_for_FULL-HEM_July10.bordercolor + '[' no = yes ']' + echo + echo + cd /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99 + '[' L = R ']' + '[' no = yes ']' + caret_command -surface-register-sphere-spec-only N /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/Macaque.TEMPLATE.FS-to-F99.LVD.deform_map 120810MILO.L.For-Reg-with-F99.78317.spec /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/Macaque.F99.R.For-Registration-with-120810MILO.L.74k_f99.spec Src/Tgt Different Hemispheres Color ??? specified multiple times with different color components. Using (170,170,170,2) Color ??? specified multiple times with different color components. Using (170,170,170,2) Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. Point is on nearest node. 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WARNING: coordinate file F99-registered.120810MILO.L.Midthickness_MWS.74k_f99.coord has 2361 crossovers after deformation. WARNING: coordinate file F99-registered.120810MILO.L.INFLATED.74k_f99.coord has 6206 crossovers after deformation. WARNING: coordinate file F99-registered.120810MILO.L.SPHERICAL_STD.74k_f99.coord has 56666 crossovers after deformation. + rm '*sphere_stage_*coord' rm: cannot remove `*sphere_stage_*coord': No such file or directory + cd /Freiwald/jsliwa/cooked/anatomicals/FS_to_caret_F99/F99_TARGET/ + cat + mkdir TEMP_RENAME mkdir: cannot create directory `TEMP_RENAME': File exists + mkdir BAK_RENAME mkdir: cannot create directory `BAK_RENAME': File exists + cp F99-registered.120810MILO.L.74k_f99.surface_shape F99-registered.120810MILO.L.For-Reg-with-F99.74k_f99.spec F99-registered.120810MILO.L.INFLATED.74k_f99.coord F99-registered.120810MILO.L.LANDMARKS.74k_f99.borderproj F99-registered.120810MILO.L.Midthickness_MWS.74k_f99.coord F99-registered.120810MILO.L.SPHERICAL_STD.74k_f99.coord BAK_RENAME + mv F99-registered.120810MILO.L.74k_f99.surface_shape F99-registered.120810MILO.L.For-Reg-with-F99.74k_f99.spec F99-registered.120810MILO.L.INFLATED.74k_f99.coord F99-registered.120810MILO.L.LANDMARKS.74k_f99.borderproj F99-registered.120810MILO.L.Midthickness_MWS.74k_f99.coord F99-registered.120810MILO.L.SPHERICAL_STD.74k_f99.coord TEMP_RENAME + cp rename_F99-registered.sh TEMP_RENAME + cp rename_NUMBER_NODES-to-74k_f99.sh TEMP_RENAME + cd TEMP_RENAME + sh rename_F99-registered.sh Replacing: F99-registered. With: Affected file: F99-registered.120810MILO.L.74k_f99.surface_shape Affected file: F99-registered.120810MILO.L.For-Reg-with-F99.74k_f99.spec Affected file: F99-registered.120810MILO.L.INFLATED.74k_f99.coord Affected file: F99-registered.120810MILO.L.LANDMARKS.74k_f99.borderproj Affected file: F99-registered.120810MILO.L.Midthickness_MWS.74k_f99.coord Affected file: F99-registered.120810MILO.L.SPHERICAL_STD.74k_f99.coord Affected file: rename_F99-registered.sh mv F99-registered.120810MILO.L.74k_f99.surface_shape 120810MILO.L.74k_f99.surface_shape mv F99-registered.120810MILO.L.For-Reg-with-F99.74k_f99.spec 120810MILO.L.For-Reg-with-F99.74k_f99.spec mv F99-registered.120810MILO.L.INFLATED.74k_f99.coord 120810MILO.L.INFLATED.74k_f99.coord mv F99-registered.120810MILO.L.LANDMARKS.74k_f99.borderproj 120810MILO.L.LANDMARKS.74k_f99.borderproj mv F99-registered.120810MILO.L.Midthickness_MWS.74k_f99.coord 120810MILO.L.Midthickness_MWS.74k_f99.coord mv F99-registered.120810MILO.L.SPHERICAL_STD.74k_f99.coord 120810MILO.L.SPHERICAL_STD.74k_f99.coord mv rename_F99-registered.sh rename_sh + sh rename_NUMBER_NODES-to-74k_f99.sh Replacing: 73730. With: 74k_f99. Affected file: 120810MILO.L.74k_f99.surface_shape Affected file: 120810MILO.L.INFLATED.74k_f99.coord Affected file: 120810MILO.L.Midthickness_MWS.74k_f99.coord Affected file: 120810MILO.L.SPHERICAL_STD.74k_f99.coord Affected file: rename_NUMBER_NODES-to-74k_f99.sh mv *73730.* 120810MILO.L.74k_f99.surface_shape 120810MILO.L.74k_f99.surface_shape.rev 120810MILO.L.For-Reg-with-F99.74k_f99.spec 120810MILO.L.INFLATED.74k_f99.coord 120810MILO.L.INFLATED.74k_f99.coord.rev 120810MILO.L.LANDMARKS.74k_f99.borderproj 120810MILO.L.Midthickness_MWS.74k_f99.coord 120810MILO.L.Midthickness_MWS.74k_f99.coord.rev 120810MILO.L.SPHERICAL_STD.74k_f99.coord 120810MILO.L.SPHERICAL_STD.74k_f99.coord.rev rename_NUMBER_NODES-to-74k_f99.sh rename_NUMBER_NODES-to-74k_f99.sh.rev mv: target `rename_NUMBER_NODES-to-74k_f99.sh.rev' is not a directory + mv 120810MILO.L.74k_f99.surface_shape 120810MILO.L.74k_f99.surface_shape.rev 120810MILO.L.For-Reg-with-F99.74k_f99.spec 120810MILO.L.INFLATED.74k_f99.coord 120810MILO.L.INFLATED.74k_f99.coord.rev 120810MILO.L.LANDMARKS.74k_f99.borderproj 120810MILO.L.Midthickness_MWS.74k_f99.coord 120810MILO.L.Midthickness_MWS.74k_f99.coord.rev 120810MILO.L.SPHERICAL_STD.74k_f99.coord 120810MILO.L.SPHERICAL_STD.74k_f99.coord.rev .. + cd .. + rm TEMP_RENAME/rename_NUMBER_NODES-to-74k_f99.sh TEMP_RENAME/rename_sh + rmdir TEMP_RENAME rmdir: TEMP_RENAME: Directory not empty + cp 120810MILO.L.For-Reg-with-F99.74k_f99.spec BAK_RENAME + mv 120810MILO.L.For-Reg-with-F99.74k_f99.spec 120810MILO.L.Registered-to-F99.74k_f99.spec + echo scene_file Macaque.F99.R.Reg-with-120810MILO.L.scene + sed '/scene_file Macaque.F99.TEMPLATE_LANDMARKS.scene/d' 120810MILO.L.Registered-to-F99.74k_f99.spec + mv 120810MILO.L.Registered-to-F99.74k_f99.spec.rev 120810MILO.L.Registered-to-F99.74k_f99.spec + sed '/volume_anatomy_file Macaque.F99.LR.nii.gz/d' 120810MILO.L.Registered-to-F99.74k_f99.spec + mv 120810MILO.L.Registered-to-F99.74k_f99.spec.rev 120810MILO.L.Registered-to-F99.74k_f99.spec + caret_command -surface-distortion Macaque.ATLAS.sphere.6.74k.coord 120810MILO.L.SPHERICAL_STD.74k_f99.coord Macaque.sphere_6.RIGHT_HEM.74k.topo 120810MILO.L.74k_f99.surface_shape 120810MILO.L.74k_f99.surface_shape -generate-areal-distortion -areal-distortion-column-name 'Spherical distortion deformed 120810MILO.L vs F99.R sphere' + caret_command -scene-create 120810MILO.L.Registered-to-F99.74k_f99.spec '' Macaque.F99.R.Reg-with-120810MILO.L.scene '1. 120810MILO.L registered to F99 (individual and atlas landmarks with spherical distortion map)' -surface-overlay PRIMARY PAINT 'MEDIAL.WALL (July10 Both hems)' -1 -surface-overlay UNDERLAY SURFACE_SHAPE 'Spherical distortion deformed 120810MILO.L vs F99.R sphere' -1 -show-borders -window-surface-types WINDOW_MAIN 520 500 SPHERICAL CLOSED LATERAL -window-surface-types WINDOW_2 520 500 FIDUCIAL CLOSED LATERAL --------------------------------------------- Julia Sliwa, Ph.D. Laboratory of Neural Systems The Rockefeller University 1230 York Ave, New York, NY 10065
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