hi Sarah-
i'll try my hand at what you want to do below:
I have a question about creating scripts for TkSurfer. I really know next to
nothing about scripts in general so these are rather basic questions. There
seems to be a lot of scripting commands for TkMedit but not for TkSurfer. Is
there a general list of the basic commands?
there is, just type:
tksurfer
on the command line
Open a subject
Load a surface (inflated and pial)
tksurfer subject rh inflated
tksurfer subject rh pial
#see below for how to define tcl script to tksurfer, but you can also type
#the following in the tksurfer tcl prompt:
Display the color bar
set colscalebarflag 1
in a for loop
set filelist "file1.w file2.w"
set layr 0
foreach i $filelist {
Overlay a .w file Redraw the image
set val $i
sclv_read_binary_values $layr
#maybe you want to also set thresholds for the overlay
#and change the lighting model
set fthresh 1.3
set fslope 1
set fmid 2
do_lighting_model 0.4 0.0 0.6 0.2 0.4;
Save as a .rgb image
set filestem "$sbjdir/rgb/${hemi}.$i"
puts "Taking Snapshots to $filestem";
make_lateral_view;
redraw;
setfile rgb "${filestem}_lat.rgb";
puts $rgb;
save_rgb;
rotate_brain_x 90;
redraw;
setfile rgb "${filestem}_inf.rgb";
puts $rgb;
save_rgb;
make_lateral_view;
rotate_brain_y 180;
redraw;
setfile rgb "${filestem}_med.rgb";
puts $rgb;
save_rgb;
incr layr
#you can load up to 8 or 9 layers(overlays) in tksurfer
#if you have more, tksurfer won't like you and will quit.
#alternatively, you can just not increment the layr (above)
#and keep loading in layer 0
end loop
}
Is this all done in a csh script? And then how do I run the script?
it's all in tcl. a quick way to learn is TclTutor:
http://www.msen.com/~clif/TclTutor.html
you define the .tcl script for tksurfer on the command line
foreach s ($SUBJECTS)
foreach h (rh lh)
tksurfer $s $h inflated -tcl load_ovrly_and_snaps.tcl
tksurfer $s $h pial -tcl load_ovrly_and_snaps.tcl
end
end
i hope this helps.
good luck,
--
brian t. quinn
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
