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,