Thank you a lot Donna.

Merry Christmas for you too.

Yours sincerely,

Rosalia.
El 23/12/2015 20:14, "Donna Dierker" <do...@brainvis.wustl.edu> 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 <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 version from Caret has been replaced by Workvench, but I need to give a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
> >
> >
> >
> > _______________________________________________
> > 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
>
>
> _______________________________________________
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
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