Hi Julia, I confess I don't know these scripts inside and out, but this image is enlightening:
http://brainvis.wustl.edu/pipermail/caret-users/attachments/20151222/180ba486/attachment-0001.png It looks like there is a hole in the surface at the occipital pole -- almost like perhaps Caret cut out what it thought was the medial wall, but it was really occipital cortex. But that is not the only issue with the surface. There are other holes. Have you looked at the input surface in Freesurfer? Are there holes in it? Is it in a non-standard orientation (x iincreases from left to right, y increases from posterior to anterior, z increases from inferior to superior)? Donna On Dec 22, 2015, at 7:15 PM, Julia Sliwa <jsl...@mail.rockefeller.edu> wrote: > 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. > 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. > 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. > 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. > 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. > 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 > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
