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')
