Re: [caret-users] Caret tutorials
Thank you a lot Donna. Merry Christmas for you too. Yours sincerely, Rosalia. El 23/12/2015 20:14, "Donna Dierker" 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 > 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 version from Caret has been replaced by Workvench, but I need to give a 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" > 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.bord
[caret-users] Caret tutorials
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 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" 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-b
Re: [caret-users] LEFT HEM in FS-to-F99 Tutorial
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 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.
