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: