import gl
gl.resetdefaults()
pth = '~/afni/'
#the desai atlas comes with AFNI
# if this fails, use File/OpenAFNI to set AFNI folder
gl.loadimage('TT_desai_dd_mpm+tlrc.HEAD')
#set atlas saturation to 20%
gl.minmax(0, 0, 20)
gl.overlayload(pth+'ttest.wav.t0.p3.RT_REML.L-A.allmask+tlrc.HEAD')
gl.minmax(1, 2, 5)
gl.colorname(1,'Plasma')
#make overlay translucent
gl.opacity(1, 75)
#find clusters
gl.generateclusters(1)
gl.orthoviewmm(0,0,0)
#the 'tomography' shader works well with discrete atlases
gl.shadername('Tomography')
for j in range(2):
if j == 1:
output_path = output_path + '_cutout'
output_gif_path = output_path + '.gif'
print(output_path)
if not os.path.exists(output_path):
os.mkdir(output_path)
gl.loadimage(input_path)
if i == 3: # load both subcortical and cerebellum
gl.overlayload(overlay_path)
gl.overlayload(overlay2_path)
gl.opacity(1, 40)
gl.opacity(2, 70)
gl.minmax(1, 0, 1243)
gl.minmax(2, 0, 1243)
gl.colorname(1, 'x_rain')
gl.colorname(2, 'x_rain')
#gl.fullscreen(0)
else:
gl.overlayload(overlay_path)
gl.opacity(1, 40)
gl.minmax(1, 0, 1243)
gl.colorname(1, 'x_rain')
#gl.fullscreen(0)
if j == 1:
if i < 3: