Python meshload Examples

Example #1

import gl

gl.resetdefaults()
kframesperrotation = 180
gl.meshcolor(210, 148, 148)
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('red', 1)
gl.nodethresh(1.0, 1.0)
gl.edgethresh(0.5, 1.0)
for i in range(1, kframesperrotation * 5):
    s = 0.5 + (i + 0.0) / 72
    if (s <= 1):
        gl.cameradistance(s)
    if ((i % kframesperrotation) == 0):
        rot = (i / kframesperrotation)
        if rot == 1:
            gl.shadername('metal')
        elif rot == 2:
            gl.shadername('wireframe')
        elif rot == 3:
            gl.shadername('toon')
            gl.shaderambientocclusion(0)
        else:
            gl.shadername('wire')

Example #2

File: hide_curves.py Project: leej3/surf-ice

import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152Left_smoothed.mz3')
gl.meshcurv()
gl.shadername('hidecurves')
gl.overlayload('CIT168.mz3')
gl.shaderforbackgroundonly(1)
gl.shaderadjust('curvthreshhi', 0.44)

Example #3

import gl
gl.resetdefaults()
#pth='/Users/chris/Downloads/MNI_Glasser_HCP_2019_03_26/'
#pth='/Users/chris/Downloads/MNI_Glasser_HCP_2019_03_26/'
#gl.meshload(pth+'std.141.lh.pial.gii')
#gl.overlayload(pth+'lh.std.141.Glasser.1D.dset')
#gl.overlaycolorname(1,'Random')

pth = '/Users/chris/AFNI_data6x/FT_analysis/FT/SUMA/'

#gl.meshload(pth+'std.60.rh.pial.gii')
#gl.meshload(pth+'std.60.rh.inflated.gii')
#gl.overlayload(pth+'std.141.FT_rh.MI.1D')
gl.meshload(pth + 'std.141.lh.inflated.gii')
#gl.overlayload(pth+'std.141.FT_lh.niml.M2M')

#gl.overlayload(pth+'std.60.rh.aparc.a2009s.annot.niml.dset');
#gl.overlaycolorname(1,'Random')
#gl.overlayload(pth+'std.60.rh.curv.niml.dset')

#pth='/Users/chris/Downloads/MNI_Glasser_HCP_2019_03_26/surfs/'
#gl.meshload(pth+'HCP.R_Superior_Frontal_Language_Area.k1026.gii')
#gl.overlayload(pth+'HCP.R_Superior_Frontal_Language_Area.k1026.niml.dset')

Example #4

File: startup_catani4.py Project: chanyca/surf-ice

import gl
gl.meshload('lh.pial')
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(gl.overlaycount(), -2, -3)
gl.overlayopacity(gl.overlaycount(), 20)
#create new overlay based on contour of motor map:
gl.contour(gl.overlaycount())
#next line: make border thicker
#gl.overlayminmax(gl.overlaycount(),0.1,0.1)
#next line: make border a gradient
#gl.overlayminmax(gl.overlaycount(),0.1,1.0)

Example #5

File: jstartup.py Project: henrykim1004/surf-ice

import gl
gl.resetdefaults()
gl.meshload('/Users/chris/afni/pial/lh.sphere')
gl.overlayload('/Users/chris/afni/pial/lh.HCP-MMP1.annot')
gl.atlas2node('/Users/chris/afni/pial/mynodes.node')

Example #6

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)

Example #7

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)

Example #8

File: startupj.py Project: henrykim1004/surf-ice

import gl
gl.resetdefaults()
pth='/Users/chris/Downloads/MNI_Glasser_HCP_2019_03_26/'
gl.meshload(pth+'std.141.lh.pial.gii')
#gl.overlayload(pth+'lh.std.141.Glasser.gii.dset')
#gl.overlayload(pth+'lh.std.141.Glasser_HCP.niml.dset')
gl.overlayload(pth+'lh.std.141.Glasser_HCP.lbl.niml.dset')
#gl.atlas2node('/Users/chris/afni/pial/mynodes.node')
#gl.overlayload(pth+'lh.std.141.Glasser.1D.dset')

Example #9

File: hide_curves.py Project: chanyca/surf-ice

import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152_smoothed.lh.mz3')
gl.meshcurv()
gl.shadername('hidecurves')
gl.overlayload('CIT168.mz3')
gl.shaderforbackgroundonly(1)
gl.shaderadjust('curvthreshhi', 0.44)

Example #10

File: startup_2020.py Project: chanyca/surf-ice

import gl
gl.resetdefaults()
gl.meshhemisphere(1)

#gl.meshloadbilateral(1)
#gl.hemispheredistance(0.5)
gl.meshload("/Users/chris/aa/_rh.inflated")

gl.overlayload(
    'fs7converted_fs5_sct2in_fwhm10_npc_cft3.1_rh_dpv_npc_fisher_cfdrp_d1_c1.mgz'
)
gl.overlayminmax(1, 2.301, 4)
gl.overlaycolor(1, 128, 255, 128, 255, 0, 255)

gl.overlayload(
    'fs7converted_fs5_sct2in_fwhm10_npc_cft3.1_rh_dpv_npc_fisher_cfdrp_d1_c2.mgz'
)
gl.overlayminmax(2, 2.301, 4)
gl.overlaycolor(2, 255, 0, 255, 128, 128, 128)

gl.overlayload(
    'fs7converted_fs5_sct2in_fwhm10_npc_cft3.1_rh_dpv_npc_fisher_cfdrp_d1_c3.mgz'
)
gl.overlayminmax(3, 2.301, 4)
gl.overlaycolor(3, 255, 0, 0, 128, 255, 128)

gl.overlayload(
    'fs7converted_fs5_sct2in_fwhm10_npc_cft3.1_rh_dpv_npc_fisher_cfdrp_d1_c4.mgz'
)
gl.overlayminmax(4, 2.301, 4)
gl.overlaycolor(4, 0, 0, 255, 128, 255, 128)

Example #11

File: zwatertight.py Project: henrykim1004/surf-ice

import gl
gl.resetdefaults()
gl.meshload('AICHAhr_left')
gl.atlas2node('/Users/chris/afni/pial/mynodes.node')

Example #12

import gl
gl.resetdefaults()
gl.meshload('/Users/chris/catani/fs_LR.L.inflated_va_avg.32k_fs_LR.surf.gii')
gl.overlayload('/Users/chris/catani/Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii')
gl.contour(0)

#gl.overlayload('/Users/chris/catani/Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii')

Example #13

import gl
gl.resetdefaults()
gl.meshload('mni152_2009.mz3')
gl.overlayload('motor_4t95mesh.mz3')
gl.clipazimuthelevation(0.37, 0, 140)
gl.shaderambientocclusion(0.5)
gl.azimuthelevation(90, 20)
gl.shaderxray(1.0, 0.3)

Example #14

import gl
ksteps = 100
gl.resetdefaults()
gl.meshload('stroke.mz3')
gl.trackload('stroke.trk.gz')
gl.trackprefs(15, 3, 0.5)
for i in range(1, ksteps):
    gl.clipazimuthelevation(((0.8 * i) / ksteps), 0, 130)
    gl.wait(20)

Example #15

import gl
gl.resetdefaults()
gl.meshload('/Users/chris/afni/pial/lh.pial')
gl.overlayload('/Users/chris/afni/pial/lh.HCP-MMP1.annot')
gl.atlas2node('/Users/chris/afni/pial/mynodes.node')

Example #16

import gl
gl.resetdefaults()
kframesperrotation = 180
gl.meshcolor(210, 148, 148)
gl.meshload('BrainMesh_ICBM152Left.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('red', 1)
gl.nodethresh(1.0, 1.0)
gl.edgethresh(0.5, 1.0)
for i in range(1, kframesperrotation * 5):
    s = 0.5 + (i + 0.0) / 72
    if (s <= 1):
        gl.cameradistance(s)
    if ((i % kframesperrotation) == 0):
        rot = (i / kframesperrotation)
        if rot == 1:
            gl.shadername('metal')
        elif rot == 2:
            gl.shadername('wireframe')
        elif rot == 3:
            gl.shadername('toon')
            gl.shaderambientocclusion(0)
        else:
            gl.shadername('wire')
            gl.shaderforbackgroundonly(1)

Example #17

import gl
gl.resetdefaults()
gl.meshload('lh.inflated')
#gl.overlayload(pth+'lh.std.141.Glasser.gii.dset')
#gl.overlayload(pth+'lh.std.141.Glasser_HCP.niml.dset')
gl.overlayload('boggle.annot')
#gl.atlas2node('/Users/chris/afni/pial/mynodes.node')
#gl.overlayload(pth+'lh.std.141.Glasser.1D.dset')
gl.atlas2node('/Users/chris/test.node')