import gl gl.resetdefaults() gl.meshload('BrainMesh_ICBM152Right.mz3') gl.overlayload('motor_4t95mesh.mz3') gl.overlaycolorname(1, 'red') gl.shaderxray(0.9, 0.5) gl.azimuthelevation(110, 15) gl.shadername('MatCap') gl.shadermatcap('Cortex') gl.meshcurv() gl.overlaytranslucent(2, 1)
import gl import os fnm = os.path.expanduser("~")+os.path.sep+'myLUT.clut'; f = open(fnm, "w") f.write("[INT]\n") f.write("numnodes=3\n") f.write("[BYT]\n") f.write("nodeintensity0=0\n") f.write("nodeintensity1=128\n") f.write("nodeintensity2=255\n") f.write("[RGBA255]\n") f.write("nodergba0=0|0|0|0\n") f.write("nodergba1=128|128|0|64\n") f.write("nodergba2=255|0|0|128\n") f.close() gl.meshload('BrainMesh_ICBM152.rh.mz3') gl.overlayload('motor_4t95vol.nii.gz') gl.overlaycolorname(1,fnm)
import gl gl.resetdefaults() gl.meshload('~/catani/fs_LR.L.inflated_va_avg.32k_fs_LR.surf.gii') gl.overlayload('~/catani/Wang_2015.32k_fs_LR.dlabel.nii') gl.contour(gl.overlaycount()) gl.overlaycolorname(gl.overlaycount(), 'Grayscale') #invert color scheme so borders are black not white gl.overlayinvert(gl.overlaycount(), 1)
import gl gl.resetdefaults() gl.meshload('BrainMesh_ICBM152.rh.mz3') gl.meshcurv() gl.overlayminmax(1, -1, 1) gl.overlaycolorname(1, 'surface') gl.overlayinvert(1, 1) gl.overlayload('motor_4t95vol.nii.gz') gl.overlaycolorname(2, 'kelvin') gl.overlayminmax(2, 2, 7) gl.overlayload('scalp.mz3') gl.overlaycolorname(3, 'gold') gl.shaderxray(1.0, 0.9) gl.meshoverlayorder(1) gl.colorbarvisible(0) gl.shaderambientocclusion(0.05) gl.azimuthelevation(90, 15) gl.clipazimuthelevation(0.5, 0, 90)
import gl gl.resetdefaults() #opacity adjusts whether overlays are translucent (0) opacity = 50 pth = '/Users/chris/Downloads/sf/' gl.azimuthelevation(70, 15) gl.meshload('BrainMesh_ICBM152_smoothed.mz3') gl.overlayload(pth+'bin.thr.ACC_LR.nii.gz') gl.overlaycolorname(1, 'Violet [r+b]') gl.overlayminmax(1,0.5,0.5) gl.overlayopacity(1, opacity) gl.overlayload(pth+'bin.thr.S2_OP1_LR.nii.gz') gl.overlaycolorname(2, 'Violet [r+b]') gl.overlayminmax(2,0.5,0.5) gl.overlayopacity(2, opacity) gl.overlayload(pth+'bin.thr.INS_LR.nii.gz') gl.overlaycolorname(3, 'Bronze-Gold') gl.overlayminmax(3,0.5,0.5) gl.overlayopacity(3, opacity) gl.overlayload(pth+'bin.thr.Tha_LR.nii.gz') gl.overlaycolorname(4, 'Blue') gl.overlayminmax(4,0.5,0.5) gl.overlayopacity(4, opacity) gl.overlayload(pth+'bin.thr.S1_BA2_LR.nii.gz') gl.overlaycolorname(5, 'Cyan [g+b]') gl.overlayminmax(5,0.5,0.5) gl.overlayopacity(5, opacity) gl.overlayload(pth+'thresh_zstat1.nii.gz') gl.overlaycolorname(6, 'Red') gl.overlayminmax(6,0.5,0.5) gl.overlayopacity(6, 100)
import gl gl.resetdefaults() gl.meshload('BrainMesh_ICBM152.lh.mz3') gl.edgeload('LPBA40.edge') gl.clipazimuthelevation(0.3, 0, 130) gl.nodesize(6, 1) gl.edgesize(3,1) gl.nodehemisphere(-1) gl.azimuthelevation(250, 35) gl.edgecolor('actc',1) gl.nodecolor('blue',1) gl.nodethresh(1.0,1.0) gl.edgethresh(0.5,1.0) gl.meshcurv() gl.overlayminmax(1,-1,1) gl.overlaycolorname(1,'surface') gl.overlayinvert(1,1) gl.overlaytranslucent(1, 1)
import gl gl.resetdefaults() gl.meshload('BrainMesh_ICBM152.rh.mz3') gl.overlayload('motor_4t95vol.nii.gz') gl.overlayminmax(1,2,12) gl.overlaycolorname(2, 'Red-Yellow') gl.azimuthelevation(110, 15) gl.shadername('MatCap'); gl.meshcurv() gl.overlaytranslucent(2, 1)
import gl gl.resetdefaults() gl.meshload('~/catani/fs_LR.L.inflated_va_avg.32k_fs_LR.surf.gii') gl.overlayload('~/catani/Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii') gl.contour(0) gl.atlassaturationalpha(0.9, 0.5) gl.overlaycolorname(1,'Grayscale') gl.overlayinvert(1,1);
import gl gl.resetdefaults() gl.azimuthelevation(70, 15) gl.meshload('BrainMesh_ICBM152Right.mz3') gl.overlayload('motor_4t95vol.nii.gz') gl.overlaycolorname(1, 'Gold')