Thank you a lot Donna. Merry Christmas for you too.
Yours sincerely, Rosalia. El 23/12/2015 20:14, "Donna Dierker" <[email protected]> escribió: > This message is for Rosalia, but I have changed the subject line, to keep > the previous thread focused on Julia's monkey surface issues. > > There are several Caret tutorials here: > > http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation > > This one gives you a pretty good overview, but takes a day to get through: > > Caret 5.5 Tutorial - The Basics (including PALS atlas) > > The dataset is available without Aspera hassles: > > > http://sumsdb.wustl.edu/sums/download.do?archive_id=6595030&filename=CARET_TUTORIAL_SEPT06.zip > > Click the diskette shaped icon to download the zip file. Unzip and you'll > get a bunch of data. > > The QuickStart tutorial is the next best thing, if you don't have the day > to spend on the one above. > > While people do still use Caret for many things, like the script Julia is > running for monkeys, people are moving to Workbench data formats for newer > human studies. It does depend on what you'll be doing. Diffusion analyses > will need Workbench. > > I also saw your posts on hcp-users with the Aspera issues -- sorry for > that. > > > On Dec 23, 2015, at 10:07 AM, Rosalia Dacosta Aguayo <[email protected]> > wrote: > > > Dear Julia and Donna, > > > > I have to run a Caret tutorial latest vetsion ( I have never run it, I > have just installed and I downloaded the tutorial). I know that latest > version from Caret has been replaced by Workvench, but I need to give a > first try with Caret Taking into account that U am interested in human > brains...what tutorial would you recommend me and...what about the > samples...is there any sample for Caret training that I could download > easily? > > > > I would be more than grateful if you could give me some help with this. > > > > Yours sicerely, > > Rosalia. > > > > Pd: Merry Christmas > > > > El 23/12/2015 02:21, "Julia Sliwa" <[email protected]> > escribió: > > 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 > > > > > > <image.png> > > --------------------------------------------- > > Julia Sliwa, Ph.D. > > Laboratory of Neural Systems > > The Rockefeller University > > 1230 York Ave, New York, NY 10065 > > > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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