def visualize_axial(niidir, savedir, min=0.75, max=1.0):
gl.viewaxial(1)
for method in ['grad', 'cam']:
for network in ['Vis', 'SomMot', 'DorsAttn', 'SalVentAttn', 'Limbic', 'Cont', 'Default']:
for gender in ['female', 'male']:
gl.overlayload(os.path.join(niidir, 'network', 'saliency_{}_{}_top20_{}_lh'.format(method, gender, network)))
gl.overlayload(os.path.join(niidir, 'network', 'saliency_{}_{}_top20_{}_rh'.format(method, gender, network)))
gl.minmax(1, min, max)
gl.minmax(2, min, max)
gl.colorname(1, colorname)
gl.colorname(2, colorname)
gl.savebmp(os.path.join(savedir, '{}_{}_{}_axial.png'.format(method, network, gender)))
gl.overlaycloseall()
def visualize_sagittal(niidir, savedir, min=0.75, max=1.0):
for hemisphere in ['lh', 'rh']:
if hemisphere =='lh': gl.clipazimuthelevation(0.49, 90, 0)
elif hemisphere =='rh': gl.clipazimuthelevation(0.49, 270, 0)
for network in ['Vis', 'SomMot', 'DorsAttn', 'SalVentAttn', 'Limbic', 'Cont', 'Default']:
for gender in ['female', 'male']:
gl.overlayload(os.path.join(niidir, 'network', 'saliency_{}_top20_{}_{}'.format(method, gender, network, hemisphere)))
gl.minmax(1, min, max)
gl.colorname(1, colorname)
gl.viewsagittal(1)
gl.savebmp(os.path.join(savedir, '{}_{}_sagittal_{}_lt.png'.format(network, gender, hemisphere)))
gl.viewsagittal(0)
gl.savebmp(os.path.join(savedir, '{}_{}_sagittal_{}_rt.png'.format(network, gender, hemisphere)))
gl.overlaycloseall()
# gl.colorname (1,"8redyell")
# gl.opacity(1,80)
# #gl.mosaic('l+ h -0.3 v -0.1 a 55 s x r 0')
# gl.mosaic('a 55')
# gl.colorbarposition(0)
# #gl.linewidth(5)
# gl.savebmp(OAc_filenames[this_index])
OAi_filenames=['C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/OAi_Flat', \
'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/OAi_Low', \
'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/OAi_Med', \
'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/OAi_Hard' ]
for this_index in range(0, len(OAi_filenames)):
gl.overlaycloseall()
gl.overlayload(OAi_filenames[this_index])
gl.minmax(1, 0, 5)
gl.colorname(1, "8redyell")
gl.opacity(1, 80)
#gl.mosaic('l+ h -0.3 v -0.1 a 55 s x r 0')
gl.mosaic('a 55')
gl.colorbarposition(0)
#gl.linewidth(5)
gl.savebmp(OAi_filenames[this_index])
# YA_filenames=['C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/YA_Flat', \
# 'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/YA_Low', \
# 'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/YA_Med', \
# 'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/YA_Hard' ]
# for this_index in range(0,len(YA_filenames)):
import gl
gl.resetdefaults()
#opacity adjusts whether overlays are translucent (0)
opacity = 50
pth = '/Users/chris/Downloads/sf/'
gl.meshload('BrainMesh_ICBM152_smoothed.mz3')
gl.overlayload(pth + 'region.mz3')
gl.overlayload(pth + 'stat.mz3')
gl.overlayoverlapoverwrite(0)
import gl
gl.resetdefaults()
gl.backcolor(0, 0, 0)
gl.colorbarsize(0.02)
gl.cameradistance(0.6)
# load main image
gl.loadimage('./outputs/LCT1/LCT1_brain.nii.gz')
gl.shadername('Standard')
gl.shaderadjust('surfaceColor', 1)
gl.shaderadjust('brighten', 5)
# load overlay 1
gl.overlayload(
'/Users/Bryce/Desktop/Postdoc_Scripts/GitHub/04_mosaics_data/00_Multiple_files/outputs/LCT1/LCT1_heatmap.nii.gz'
)
gl.overlayloadsmooth(1)
gl.minmax(1, 1, 50)
gl.colorname(1, "4hot")
gl.shaderadjust('overlayDepth', 0.35)
# #load overlay 2
gl.overlayload('./outputs/LCT1/LCT1_responses.nii.gz')
gl.overlayloadsmooth(1)
gl.minmax(2, 0, 50)
gl.colorname(2, "2green")
gl.shaderadjust('overlayDepth', 0.35)
# #open background image
# gl.loadimage('spm152')
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)
import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayloadsmooth(1);
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
#open overlay: show negative regions
gl.overlayloadsmooth(0);
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")
gl.overlayloadsmooth(1);
print("n.b. Blue surface is jagged (smoothing off)");
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)
rois_to_plot = ['neurosynth_acc_gmMasked', 'neurosynth_dlpfc_left_gmMasked', 'neurosynth_dlpfc_right_gmMasked']
# rois_to_plot = ['neurosynth_acc_mask', 'neurosynth_dlpfc_left_mask', 'neurosynth_dlpfc_right_mask']
# rois_to_plot = ['left_dlpfc', 'right_dlpfc', 'left_acc', 'right_acc']
######################################
gl.loadimage('//exasmb.rc.ufl.edu/blue/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/MNI_2mm.nii')
gl.opacity(1,1)
######################################
# rois_plotted=1;
# this_index=0;
for this_roi in rois_to_plot:
# gl.loadimage('//exasmb.rc.ufl.edu/blue/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/MNI_2mm.nii')
# gl.opacity(1,10)
# gl.mosaic('a -36 -32 -28 -24 -20 -16 -10 -6 -2; 2 6 10 14 18 22 26 30 34; 38 42 46 50 54 58 62 66 70')
# gl.mosaic("A R 0 C R 0 S R 0; A R -0 C R -0 S R -0");
gl.mosaic("A R 0");
gl.overlayload("//exasmb.rc.ufl.edu/blue/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/"+this_roi)
#gl.minmax(0,.01,.01)
gl.colorbarposition(0)
gl.colornode(1,2,255,0,0,255,255) # blue
gl.colornode(2,2,255,255,0,0,255) # red
gl.colornode(3,2,255,0,255,0,255) # green
# gl.colornode(4,2,255,0,88,0,255) #darkgreen
gl.backcolor(255,255,255)
gl.savebmp("//exasmb.rc.ufl.edu/blue/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/"+this_roi)
import gl
gl.resetdefaults()
#open background image
gl.loadimage('mni152')
gl.backcolor(255, 255, 255)
#open overlay:
gl.overlayloadsmooth(0)
#open overlay: sub 41, 1 site
gl.overlayload(
'/Users/mflounders/Desktop/cnds/multiplied_BLA/041sph_bin.nii.gz')
gl.minmax(1, 0, 14)
gl.colorname(1, "NIH")
#open overlay: sub 81, 1 site
gl.overlayload(
'/Users/mflounders/Desktop/cnds/multiplied_BLA/081sph_bin.nii.gz')
gl.minmax(2, 0, 14)
gl.colorname(2, "NIH")
#open overlay: sub 91, 1 site
gl.overlayload(
'/Users/mflounders/Desktop/cnds/multiplied_BLA/091sph_bin.nii.gz')
gl.minmax(3, 0, 14)
gl.colorname(3, "NIH")
#open overlay: sub 111, 3 sites
gl.overlayload(
'/Users/mflounders/Desktop/cnds/multiplied_BLA/111sph_bin.nii.gz')
gl.minmax(4, 0, 14)
gl.colorname(4, "NIH")
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')
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')
import gl
gl.meshload('lh.pial')
gl.overlayload('/Users/chris/neurovault/135002.L.func.gii')
gl.contour(0)
import gl
gl.resetdefaults()
gl.backcolor(255,255,255)
pth = '~/afni/'
gl.loadimage(pth+'FT_anat+orig.HEAD')
gl.overlayload('TSNR.FT+orig.HEAD')
gl.opacity(1, 50)
gl.extract(1,1,3)
gl.clipazimuthelevation(0.3, 0, 120)
import gl
gl.meshload('~/catani/fs_LR.L.inflated_va_avg.32k_fs_LR.surf.gii')
#load atlas
gl.overlayload(
'~/catani/Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii'
)
#make atlas translucent
gl.atlassaturationalpha(0.2, 0.5)
#show borders
gl.contour(gl.overlaycount())
gl.overlaycolorname(gl.overlaycount(), 'Grayscale')
#invert color scheme so borders are black not white
gl.overlayinvert(gl.overlaycount(), 1)
gl.overlayopacity(gl.overlaycount(), 50)
#load statistical map as image
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(gl.overlaycount(), -2, -3)
gl.overlayopacity(gl.overlaycount(), 75)
#create new overlay based on contour of motor map:
gl.contour(gl.overlaycount())
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')
#gl.overlayload("//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/Gordon2016_VentralAttn_mask")
#gl.minmax(11, 0.01,0.1)
#gl.colorname(11,'GE_color')
#gl.colorfromzero(11,1)
#gl.overlayload("//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/Gordon2016_Visual_mask")
#gl.minmax(12, 0.01,0.1)
#gl.colorname(12,'CT_Kidneys')
#gl.colorfromzero(12,1)
##Power Networks
gl.loadimage(
'//cifs.rc.ufl.edu/ufrc/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/MNI_1mm.nii'
)
gl.opacity(1, 50)
gl.overlayload(
"//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/Power2011_Auditory_mask"
)
gl.minmax(1, 0.01, 0.1)
gl.colorname(1, '1red')
gl.colorfromzero(1, 1)
gl.overlayload(
"//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/Power2011_Cingulo-opercular_Control_mask"
)
gl.minmax(2, 0.01, 0.1)
gl.colorname(2, '2green')
gl.colorfromzero(2, 1)
gl.overlayload(
"//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/Power2011_Default_mode_mask"
)
gl.minmax(3, 0.01, 0.1)
gl.colorname(3, '3blue')
import gl
gl.meshload('lh.pial')
gl.overlayload('boggle.annot')
gl.contour(0)
help(gl)
# Load main image and overlay
mep_path = os.path.join('C:/', 'Users', 'Enzon', 'Documents', 'Projects',
'MEP', 'mep-scripts')
reference_path = os.path.join(mep_path, 'Data', 'Mouse', 'Reference')
analysis_path = os.path.join(mep_path, 'Data', 'Mouse', 'Analysis')
main_path = os.path.join(reference_path,
'average_template_50_reoriented.nii.gz')
overlay1_path = os.path.join(
analysis_path, 'annotation_50_reoriented_pVal_inv_sig_volIncrease.nii.gz')
overlay2_path = os.path.join(
analysis_path, 'annotation_50_reoriented_pVal_inv_sig_volDecrease.nii.gz')
gl.loadimage(main_path)
gl.overlayload(overlay1_path)
gl.overlayload(overlay2_path)
gl.opacity(1, 50)
gl.opacity(2, 50)
gl.minmax(1, 0, 3)
gl.minmax(2, 0, 3)
gl.colorname(1, '1red')
gl.colorname(2, '3blue')
output_dir_path = os.path.join(analysis_path, 'imageSequenceFolders',
'pVal_inv_sig_InDe')
if not os.path.exists(output_dir_path):
os.mkdir(output_dir_path)
y_min = -13.15
y_max = 0
y_step = 0.05
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() pth = '~/afni/' gl.loadimage(pth+'fitts.FT+orig.HEAD') gl.overlayload(pth+'stats.FT+orig.HEAD') gl.loadgraph(pth+'ideal_Arel.1D', 0) gl.loadgraph(pth+'ideal_Vrel.1D', 1) gl.graphscaling(3) gl.volume(1,8) gl.minmax(1, 6, 12) gl.colorname(1,'Viridis') gl.generateclusters(1) gl.orthoviewmm(0,0,0)
import gl
gl.resetdefaults()
gl.meshload('lh.pial')
gl.overlayload('boggle.lh.annot')
#make contour at border of atlas
gl.contour(0)
#reduce atlas salience:
gl.atlassaturationalpha(0.2, 0.5)
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(gl.overlaycount(), -2, -3)
#hide statistical map:
gl.overlayopacity(gl.overlaycount(), 0)
#draw outline of statistical threshold
gl.contour(gl.overlaycount())
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
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)
print(gl.version())
gl.resetdefaults()
#gl.loadimage('//cifs.rc.ufl.edu/ufrc/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/Template_4_IXI555_MNI152_GS.nii')
gl.loadimage(
'//cifs.rc.ufl.edu/ufrc/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/MNI_2mm.nii'
)
OA_filename = [
'//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/Level2_Results/MRI_files/05_MotorImagery/oldadult/spmT_0001.nii'
]
#OA_filename = ['//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/Level2_Results/MRI_files/05_MotorImagery/oldadult/spmT_0002.nii']
#OA_filename = ['//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/Level2_Results/MRI_files/05_MotorImagery/oldadult/spmT_0003.nii']
#OA_filename = ['//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/Level2_Results/MRI_files/05_MotorImagery/oldadult/spmT_0004.nii']
#OA_filename = ['//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/Level2_Results/MRI_files/05_MotorImagery/oldadult/spmT_0005.nii']
gl.overlayload(OA_filename[0])
gl.minmax(1, 1, 5)
gl.colorname(1, "8redyell")
gl.opacity(1, 80)
#gl.mosaic('l+ h -0.3 v -0.1 a 55 s x r 0')
gl.mosaic('a 55')
gl.colorbarposition(0)
#gl.linewidth(5)
gl.savebmp(OA_filename[0])
gl.loadimage(
'//cifs.rc.ufl.edu/ufrc/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/MNI_2mm.nii'
)
YA_filename = [
'//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/Level2_Results/MRI_files/05_MotorImagery/youngadult/spmT_0001.nii'
]
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_ICBM152Left_smoothed.mz3')
gl.meshcurv()
gl.shadername('hidecurves')
gl.overlayload('CIT168.mz3')
gl.shaderforbackgroundonly(1)
gl.shaderadjust('curvthreshhi', 0.44)
import gl
gl.resetdefaults()
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('aal')
gl.scriptformvisible(1)
#gl.atlashide(1)
#gl.atlasshow(1, 17)
gl.atlasshow(1, (22, 23, 17))
mx = gl.atlasmaxindex(1)
print(mx)
#gl.opacity(1,50)
#
# if (layer > 0) then
# Vol1.UpdateOverlays(vols);
#str = gl.atlaslabels(1)
#print(str)
#gl.minmax(1, 4, 100)
#gl.overlayload('aal')
#
#gl.generateclusters(0)
#gl.generateclusters(0, 0.5, 32, 1, 0)
# %% overlay ----------------------
FILESPATH='D:\\GD_UNICAMP\\IC_NeuroFisica\\Projetos\\fMRI_TLE_2020\\Seed_based_analysis'
os.chdir(FILESPATH)
networks_names=['DMN','SMOTOR','VISUAL','AUDIT','ECN_L','ECN_R']
netfile_sufx= ['_Group1X','_Group2L','_Group3R','_Group4N']
for net in networks_names:
savefolder=FILESPATH + '\\' + net + '\\'
for i in netfile_sufx:
FILENAME=net+i
SEEDFILENAME=net+"_seed"
gl.overlaycloseall()
gl.overlayload(FILENAME)
gl.overlayload(SEEDFILENAME)
gl.colorname (2,"3blue")
#gl.opacity(1,50)
# changing view ----------------------
gl.azimuthelevation(140,20)
ktime= 1
ksteps= 72
for x in range(0, ksteps):
gl.azimuthelevation(140+(x*5),20)
gl.wait(ktime)
if x < 10:
gl.savebmp(savefolder + FILENAME + '_0' + str(x)+'.png')
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')