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 the < > is 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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Freesurfer@nmr.mgh.harvard.edu
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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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