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 <rdacos...@gmail.com> 
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 from Caret has been replaced by Workvench, but I need to give a first try 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" <jsl...@mail.rockefeller.edu> 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
> 
> 
> 
> _______________________________________________
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> caret-users@brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> 
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