Re: [Freesurfer] tcl script - rotate and save graphics
Hi Daniel et al.,
thanks for the rotate and save_tiff script. I've installed the dev
version (redhat 9 download onto Debian sarge) and the script works
well. I would like to set the resolution of the .tif output files (eg,
600 dpi), can we do that?
I have a problem when using a label in the tcl script (see example.tcl
below). I can startup tksurfer from the csh prompt, create a label,
save it, exit, start again, load the label, and it displays correctly.
So I assume all the label tools are working. When I restart with -tcl
example.tcl, tksurfer draws an entirely blue surface after loading the
label (any label). Have you seen this before? Am I doing something
wrong? Should I source the tksurfer.tcl script, at the beginning of
this script, to get all the lighting etc. correct? I tried to startup
tksurfer normally, with no explicit -tcl option, and then source
example.tcl at the tcl prompt, but the entire surface turns blue after
the script loads a label. Can you replicate this or advise me how to
avoid it?
Is it possible to create a shell script or a tcl script that can startup
tksurfer and run a specific tcl script across a group of subjects?
Thanks, Darren
##
# START EXAMPLE.TCL SCRIPT
set SUBJECTS_DIR /usr/local/freesurfer/subjects
set subjID ucsf_cj
set subjPath [ file join ${SUBJECTS_DIR} ${subjID} ]
set subjSurfPath [ file join ${subjPath} surf ]
set subjLabelPath [ file join ${subjPath} label ]
set subjTiffPath [ file join ${subjPath} rgb ]
foreach h {lh} {
# ---
# load the inflated surface, with curvature
set insurf [file join ${subjSurfPath} ${h}.inflated]
read_binary_surf
set curv [file join ${subjSurfPath} ${h}.curv]
read_binary_curv
UpdateAndRedraw
# ---
# load and display relevant .label files
set labels [ glob -directory ${subjLabelPath} ${h}_test.label ]
foreach l $labels {
puts loading label: $l
labl_load $l
# AT THIS POINT WE HAVE AN ENTIRELY BLUE SURFACE
}
# now rotate and save the views ...
}
# END TCL SCRIPT
##
Best, Darren
Daniel Goldenholz wrote:
Hi Darren and other Freesurfers
I wrote a tcl script to do just what was described. The one I made
gives the flexibility to name the tiff files based on a prefix that
you specify before
running the script. This way you run the same exact script for as many
pictures as you like, simply changing the prefix before running the
script.
Here is what you do. In tksurfer, after you have set up whatever
overlays and/or labels and/or surfaces etc that you like, you enter at
the command prompt
set pre whatever-you-want
(where the stuff inside theis any file prefix... for instance,
set pre bold_contrast1 )
then you run the following tcl script via the menu for running a
script...
UpdateAndRedraw
puts Taking Snapshots...
make_lateral_view
rotate_brain_y 90
redraw
set tiff ${pre}_bck.tif
save_tiff $tiff
make_lateral_view
redraw
set tiff ${pre}_lat.tif
save_tiff $tiff
rotate_brain_y 180
redraw
set tiff ${pre}_med.tif
save_tiff $tiff
make_lateral_view
rotate_brain_x 90
redraw
set tiff ${pre}_inf.tif
save_tiff $tiff
rotate_brain_x 180
redraw
set tiff ${pre}_sup.tif
save_tiff $tiff
make_lateral_view
rotate_brain_y 270
redraw
set tiff ${pre}_front.tif
save_tiff $tiff
Darren Weber wrote:
Hi Bruce etal,
I would like a short tcl script to rotate each hemisphere through all
the main views (lateral, medial, dorsal, ventral, anterior,
posterior) and output a graphics file with the name of the subject
and the view in the file name. I've found rotate_brain_[xyz] and
save_rgb, but the latter does not permit a file name for the output
graphics. I would like high-resolution graphics for publications,
but the save_rgb outputs about 85-90 dpi images. Is there an option
for vector graphics or high resolution tiff or png images?
Best, Darren
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--
Darren L. Weber, Ph.D.
Visiting Postdoctoral Scholar
Dynamic Neuroimaging Laboratory, Department of Radiology,
University of California, San Francisco,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.
Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber
To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself.
--Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
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Re: [Freesurfer] tcl script - rotate and save graphics
Sorry, there's no way to change the resolution of the TIFF
images. However, we don't supersample when taking screen shots, so
just make the window as big as you can, take the TIFF, and then you
can use an image conversion program to change the DPI.
I don't think you want to use read_binary_surf. If you're just trying
to load a single vertex set in addition to the ones you've already
loaded, use this function:
read_surface_vertex_set field fileName
Reads a set of vertices from the fle in fileName. field should
be one of the following:
0 Main vertices
1 Inflated vertices
2 White vertices
3 Pial vertices
4 Orig vertices
I was having your problem until I replaced read_binary_surf with
read_surface_vertex_set, then labl_load works as expected.
On Sun, Feb 26, 2006 at 07:19:22PM -0800, Darren Weber wrote:
Hi Daniel et al.,
thanks for the rotate and save_tiff script. I've installed the dev
version (redhat 9 download onto Debian sarge) and the script works
well. I would like to set the resolution of the .tif output files (eg,
600 dpi), can we do that?
I have a problem when using a label in the tcl script (see example.tcl
below). I can startup tksurfer from the csh prompt, create a label,
save it, exit, start again, load the label, and it displays correctly.
So I assume all the label tools are working. When I restart with -tcl
example.tcl, tksurfer draws an entirely blue surface after loading the
label (any label). Have you seen this before? Am I doing something
wrong? Should I source the tksurfer.tcl script, at the beginning of
this script, to get all the lighting etc. correct? I tried to startup
tksurfer normally, with no explicit -tcl option, and then source
example.tcl at the tcl prompt, but the entire surface turns blue after
the script loads a label. Can you replicate this or advise me how to
avoid it?
Is it possible to create a shell script or a tcl script that can startup
tksurfer and run a specific tcl script across a group of subjects?
Thanks, Darren
##
# START EXAMPLE.TCL SCRIPT
set SUBJECTS_DIR /usr/local/freesurfer/subjects
set subjID ucsf_cj
set subjPath [ file join ${SUBJECTS_DIR} ${subjID} ]
set subjSurfPath [ file join ${subjPath} surf ]
set subjLabelPath [ file join ${subjPath} label ]
set subjTiffPath [ file join ${subjPath} rgb ]
foreach h {lh} {
# ---
# load the inflated surface, with curvature
set insurf [file join ${subjSurfPath} ${h}.inflated]
read_binary_surf
set curv [file join ${subjSurfPath} ${h}.curv]
read_binary_curv
UpdateAndRedraw
# ---
# load and display relevant .label files
set labels [ glob -directory ${subjLabelPath} ${h}_test.label ]
foreach l $labels {
puts loading label: $l
labl_load $l
# AT THIS POINT WE HAVE AN ENTIRELY BLUE SURFACE
}
# now rotate and save the views ...
}
# END TCL SCRIPT
##
Best, Darren
Daniel Goldenholz wrote:
Hi Darren and other Freesurfers
I wrote a tcl script to do just what was described. The one I made
gives the flexibility to name the tiff files based on a prefix that
you specify before
running the script. This way you run the same exact script for as many
pictures as you like, simply changing the prefix before running the
script.
Here is what you do. In tksurfer, after you have set up whatever
overlays and/or labels and/or surfaces etc that you like, you enter at
the command prompt
set pre whatever-you-want
(where the stuff inside theis any file prefix... for instance,
set pre bold_contrast1 )
then you run the following tcl script via the menu for running a
script...
UpdateAndRedraw
puts Taking Snapshots...
make_lateral_view
rotate_brain_y 90
redraw
set tiff ${pre}_bck.tif
save_tiff $tiff
make_lateral_view
redraw
set tiff ${pre}_lat.tif
save_tiff $tiff
rotate_brain_y 180
redraw
set tiff ${pre}_med.tif
save_tiff $tiff
make_lateral_view
rotate_brain_x 90
redraw
set tiff ${pre}_inf.tif
save_tiff $tiff
rotate_brain_x 180
redraw
set tiff ${pre}_sup.tif
save_tiff $tiff
make_lateral_view
rotate_brain_y 270
redraw
set tiff ${pre}_front.tif
save_tiff $tiff
Darren Weber wrote:
Hi Bruce etal,
I would like a short tcl script to rotate each hemisphere through all
the main views (lateral, medial, dorsal, ventral, anterior,
posterior) and output a graphics file with the name of the subject
and the view in the file name. I've found rotate_brain_[xyz] and
save_rgb, but the latter does not permit a file name for the output
graphics. I would like high-resolution graphics for publications,
but the save_rgb
Re: [Freesurfer] tcl script - rotate and save graphics
Hi Kevin,
I tried this alterate command, however, the main window continues to
display the orig surface, given
tksurfer -subjid rh orig
It doesn't automatically update the view for the new data in $field.
Using the 'UpdateAndRedraw' command and the 'redraw' commands do not
change the surface view.
Take care, Darren
Kevin Teich wrote:
Sorry, there's no way to change the resolution of the TIFF
images. However, we don't supersample when taking screen shots, so
just make the window as big as you can, take the TIFF, and then you
can use an image conversion program to change the DPI.
I don't think you want to use read_binary_surf. If you're just trying
to load a single vertex set in addition to the ones you've already
loaded, use this function:
read_surface_vertex_set field fileName
Reads a set of vertices from the fle in fileName. field should
be one of the following:
0 Main vertices
1 Inflated vertices
2 White vertices
3 Pial vertices
4 Orig vertices
I was having your problem until I replaced read_binary_surf with
read_surface_vertex_set, then labl_load works as expected.
On Sun, Feb 26, 2006 at 07:19:22PM -0800, Darren Weber wrote:
Hi Daniel et al.,
thanks for the rotate and save_tiff script. I've installed the dev
version (redhat 9 download onto Debian sarge) and the script works
well. I would like to set the resolution of the .tif output files (eg,
600 dpi), can we do that?
I have a problem when using a label in the tcl script (see example.tcl
below). I can startup tksurfer from the csh prompt, create a label,
save it, exit, start again, load the label, and it displays correctly.
So I assume all the label tools are working. When I restart with -tcl
example.tcl, tksurfer draws an entirely blue surface after loading the
label (any label). Have you seen this before? Am I doing something
wrong? Should I source the tksurfer.tcl script, at the beginning of
this script, to get all the lighting etc. correct? I tried to startup
tksurfer normally, with no explicit -tcl option, and then source
example.tcl at the tcl prompt, but the entire surface turns blue after
the script loads a label. Can you replicate this or advise me how to
avoid it?
Is it possible to create a shell script or a tcl script that can startup
tksurfer and run a specific tcl script across a group of subjects?
Thanks, Darren
##
# START EXAMPLE.TCL SCRIPT
set SUBJECTS_DIR /usr/local/freesurfer/subjects
set subjID ucsf_cj
set subjPath [ file join ${SUBJECTS_DIR} ${subjID} ]
set subjSurfPath [ file join ${subjPath} surf ]
set subjLabelPath [ file join ${subjPath} label ]
set subjTiffPath [ file join ${subjPath} rgb ]
foreach h {lh} {
# ---
# load the inflated surface, with curvature
set insurf [file join ${subjSurfPath} ${h}.inflated]
read_binary_surf
set curv [file join ${subjSurfPath} ${h}.curv]
read_binary_curv
UpdateAndRedraw
# ---
# load and display relevant .label files
set labels [ glob -directory ${subjLabelPath} ${h}_test.label ]
foreach l $labels {
puts loading label: $l
labl_load $l
# AT THIS POINT WE HAVE AN ENTIRELY BLUE SURFACE
}
# now rotate and save the views ...
}
# END TCL SCRIPT
##
Best, Darren
Daniel Goldenholz wrote:
Hi Darren and other Freesurfers
I wrote a tcl script to do just what was described. The one I made
gives the flexibility to name the tiff files based on a prefix that
you specify before
running the script. This way you run the same exact script for as many
pictures as you like, simply changing the prefix before running the
script.
Here is what you do. In tksurfer, after you have set up whatever
overlays and/or labels and/or surfaces etc that you like, you enter at
the command prompt
set pre whatever-you-want
(where the stuff inside theis any file prefix... for instance,
set pre bold_contrast1 )
then you run the following tcl script via the menu for running a
script...
UpdateAndRedraw
puts Taking Snapshots...
make_lateral_view
rotate_brain_y 90
redraw
set tiff ${pre}_bck.tif
save_tiff $tiff
make_lateral_view
redraw
set tiff ${pre}_lat.tif
save_tiff $tiff
rotate_brain_y 180
redraw
set tiff ${pre}_med.tif
save_tiff $tiff
make_lateral_view
rotate_brain_x 90
redraw
set tiff ${pre}_inf.tif
save_tiff $tiff
rotate_brain_x 180
redraw
set tiff ${pre}_sup.tif
save_tiff $tiff
make_lateral_view
rotate_brain_y 270
redraw
set tiff ${pre}_front.tif
save_tiff $tiff
Darren Weber wrote:
Hi Bruce etal,
I would like a short tcl script to rotate each hemisphere through all
the main views (lateral, medial, dorsal, ventral, anterior,
posterior) and output a graphics file with the name of the subject
and the
Re: [Freesurfer] tcl script - rotate and save graphics
If you are using a recent dev version of tksurfer, then try the function: save_tiff filename If you enter this into the shell and it doesn't work, then you have an older version. Our new release will have this function. There is (finally) some documentation for scripting commands in tksurfer, although it is for the newer dev version. https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferScripting I would like a short tcl script to rotate each hemisphere through all the main views (lateral, medial, dorsal, ventral, anterior, posterior) and output a graphics file with the name of the subject and the view in the file name. I've found rotate_brain_[xyz] and save_rgb, but the latter does not permit a file name for the output graphics. I would like high-resolution graphics for publications, but the save_rgb outputs about 85-90 dpi images. Is there an option for vector graphics or high resolution tiff or png images? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tcl script - rotate and save graphics
Hi Darren and other Freesurfers
I wrote a tcl script to do just what was described. The one I made gives
the flexibility to name the tiff files based on a prefix that you
specify before
running the script. This way you run the same exact script for as many
pictures as you like, simply changing the prefix before running the script.
Here is what you do. In tksurfer, after you have set up whatever
overlays and/or labels and/or surfaces etc that you like, you enter at
the command prompt
set pre whatever-you-want
(where the stuff inside theis any file prefix... for instance, set
pre bold_contrast1 )
then you run the following tcl script via the menu for running a script...
UpdateAndRedraw
puts Taking Snapshots...
make_lateral_view
rotate_brain_y 90
redraw
set tiff ${pre}_bck.tif
save_tiff $tiff
make_lateral_view
redraw
set tiff ${pre}_lat.tif
save_tiff $tiff
rotate_brain_y 180
redraw
set tiff ${pre}_med.tif
save_tiff $tiff
make_lateral_view
rotate_brain_x 90
redraw
set tiff ${pre}_inf.tif
save_tiff $tiff
rotate_brain_x 180
redraw
set tiff ${pre}_sup.tif
save_tiff $tiff
make_lateral_view
rotate_brain_y 270
redraw
set tiff ${pre}_front.tif
save_tiff $tiff
Darren Weber wrote:
Hi Bruce etal,
I would like a short tcl script to rotate each hemisphere through all the main
views (lateral, medial, dorsal, ventral, anterior, posterior) and output a
graphics file with the name of the subject and the view in the file name. I've
found rotate_brain_[xyz] and save_rgb, but the latter does not permit a file
name for the output graphics. I would like high-resolution graphics for
publications, but the save_rgb outputs about 85-90 dpi images. Is there an
option for vector graphics or high resolution tiff or png images?
Best, Darren
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--
Daniel Goldenholz
-
Cell: 617-935-9421 http://people.bu.edu/danielg/
Mavet v'chaim b'yad halashon
Life and death are in the hands of language
- Proverbs 18:21
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