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Hi, Darren, I once made an animated gif of a rotating brain showing some freesurfer results. I did this with two scripts. The first is a tcl script that was passed to tksurfer; it rotates the brain and saves the resulting images. The second is a shell script that uses imagemagik to convert all of the resulting rgb images into one animated gif. I am attaching the scripts. Please be aware, however, that the tcl script isn't very elegent. I'm actually a little embarassed by it. Also, both scripts are set up for my file system, you will need to edit a few of the settings to get them to work for you. The tcl script is based on an earlier one I saw on the mailing list, I think it was Doug Greve's, but I'm not sure. I don't give credit in the script itself, sorry for the oversight! +glenn -- It is not an aesthetic process; it's a form of magic that interposes itself between us and the hostile universe, a means of seizing power by imposing a form on our terrors as well as on our desires. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:) |
# snapshot.tcl
#
# tcl script for making pics using tksurfer.
#
# This script automates a set of tksurfer commands.
#
# Be sure to check the base directory and the
# regular expression before running!
#
# Pictures will be put in the images directory
# underneath the basedir.
#
# You may also want to adjust the thresholds
# and lighting models.
#
# glenn, sept 2005
##########################################
# To use: Set all the parameters and then
# pass the script as an argument to tksurfer
# for example:
# tksurfer average7 lh inflated -tcl snapshots.tcl
#
# The basedir is where all the w files are found
# You probably need to set this to the correct value
set basedir "/home/DARREN/MY_ANALYSIS/"
# Use a regular expression to find all of the
# *.w files for each hemisphere
foreach wfile [glob ${hemi}*.w] {
# read the wfile
set layr 0
set val "${basedir}/${wfile}"
sclv_read_binary_values $layr
# set thresholds for the overlay
# and values for the lighting model
set fthresh 1
set fslope 1
set fmid 2
do_lighting_model 0.6 0.9 0.6 0.2 0.4;
# Make and save .rgb images
set cnt 1
set imagename [string trim $wfile .w]
set filestem "/${basedir}/images/${imagename}"
puts "Taking Snapshots to $filestem";
make_lateral_view; # sets to default orientation
redraw;
set filestem "/${basedir}/images/${cnt}_${imagename}"
setfile rgb "${filestem}.rgb";
puts $rgb;
save_rgb;
# rotate up
set i 0
while {$i < 110} {
rotate_brain_x -1;
incr i 1;
incr cnt 1;
redraw;
set filestem "/${basedir}/images/${cnt}_${imagename}"
setfile rgb "${filestem}.rgb";
puts $rgb;
save_rgb;
}
# rotate down/towards
set i 0
while {$i < 90} {
rotate_brain_x 1;
rotate_brain_y -1;
rotate_brain_z 1;
incr i 1;
incr cnt 1;
redraw;
set filestem "/${basedir}/images/${cnt}_${imagename}"
setfile rgb "${filestem}.rgb";
puts $rgb;
save_rgb;
}
# rotate down/away
set i 0
while {$i < 20} {
rotate_brain_x -1;
rotate_brain_y 1;
incr i 1;
incr cnt 1;
redraw;
set filestem "/${basedir}/images/${cnt}_${imagename}"
setfile rgb "${filestem}.rgb";
puts $rgb;
save_rgb;
}
# rotate away
make_lateral_view;
rotate_brain_y -90;
set i 0
set j 0
while {$i < 100} {
rotate_brain_y 2;
if {$j < 20 && $j > -1} {
rotate_brain_x 1;
rotate_brain_z -1;}
if {$j >= 30 && $j < 50} {
rotate_brain_x -1;
rotate_brain_z 1;}
if {$j == 60} {
set j -10;}
if {$i > 79} { set j 3}
incr j 1;
incr i 1;
incr cnt 1;
redraw;
set filestem "/${basedir}/images/${cnt}_${imagename}"
setfile rgb "${filestem}.rgb";
puts $rgb;
save_rgb;
}
# rotate up
set i 0
while {$i < 40} {
rotate_brain_x 1;
rotate_brain_y -1;
rotate_brain_z -1;
incr i 1;
incr cnt 1;
redraw;
set filestem "/${basedir}/images/${cnt}_${imagename}"
setfile rgb "${filestem}.rgb";
puts $rgb;
save_rgb;
}
# rotate up
set i 0
while {$i < 40} {
# rotate_brain_x -1;
rotate_brain_y -1;
rotate_brain_z -1;
incr i 1;
incr cnt 1;
redraw;
set filestem "/${basedir}/images/${cnt}_${imagename}"
setfile rgb "${filestem}.rgb";
puts $rgb;
save_rgb;
}
# and back home
#set i 0
while {$i < 90} {
rotate_brain_x -1;
# rotate_brain_y -1;
rotate_brain_z -1;
incr i 1;
incr cnt 1;
redraw;
set filestem "/${basedir}/images/${cnt}_${imagename}"
setfile rgb "${filestem}.rgb";
puts $rgb;
save_rgb;
}
}
exit
immagic.sh
Description: application/shellscript
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