def visualize_colorbar(savedir, min=0.75, max=1.0): gl.resetdefaults() gl.minmax(0, min, max) gl.colorname(0, colorname) gl.opacity(0, 0) gl.colorbarposition(1) gl.savebmp(os.path.join(savedir, 'colorbar.png'))
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()
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') else: gl.savebmp(savefolder + FILENAME + '_' + str(x)+'.png')
#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' ] #YA_filename = ['//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/Level2_Results/MRI_files/05_MotorImagery/youngadult/spmT_0002.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_0003.nii']
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)
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 y = y_min count = 0 while y <= y_max: print(y) count = count + 1
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")
print(subject_path_list) for subject_path in subject_path_list: subject = subject_path.split(os.sep)[-1] main_path = os.path.join(subject_path, subject+'_reoriented.nii.gz') overlay1_path = os.path.join(subject_path, subject+'_annotation_orsuit_thrarg_adjusted_lobular_mc.nii.gz') gl.loadimage(main_path) gl.overlayloadsmooth(0) gl.overlayload(overlay1_path) gl.opacity(1, 50) gl.minmax(1, 0, 34) gl.colorname(1, 'x_rain') output_dir_path = os.path.join(analysis_path, 'imageSequenceFolders', subject+'_orthoview') if not os.path.exists(output_dir_path): os.mkdir(output_dir_path) if subject == 'patient': y_min = -84 y_max = -14 else: y_min = -80 y_max = -10 y_step = 1 y = y_min
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') # #open overlay: show positive regions # gl.overlayload('spmMotor') # gl.minmax(1, 4, 4) # gl.opacity(1,50)
import gl gl.resetdefaults() gl.view(16) #open background image gl.loadimage('spm152') #open overlay: show positive regions gl.overlayload('spmMotor') gl.minmax(1, -4, 4) gl.colorname(1, 'blue2red') gl.opacity(1, 80) gl.orthoviewmm(0, 0, 60) gl.zerointensityinvisible(1, 1)
import gl gl.resetdefaults() #open background image gl.loadimage('spm152') gl.overlayloadsmooth(1) #open overlay: show positive regions gl.overlayload('spmMotor') gl.minmax(1, -2, -5) gl.colorname(1, '8redyell') gl.colorfromzero(1, 1) gl.overlayload('spmMotor') gl.minmax(2, 2, 5) gl.colorname(2, '5winter') gl.colorfromzero(2, 1) gl.hiddenbycutout(1, 1) gl.cutout(0.5, 0.5, 0.5, 0, 1, 1) gl.shadername('OverlaySurface') gl.backcolor(255, 255, 255)
import gl gl.resetdefaults() gl.loadimage('CT_Philips') gl.colorname(0, 'CT_Kidneys') gl.shadername('Tomography') gl.azimuthelevation(150, 10) gl.clipazimuthelevation(0.25, 180, 60)
import gl import sys print(sys.version) print(gl.version()) # gl.resetdefaults() help(gl) gl.linewidth(3) gl.opacity(1, 40) gl.opacity(2, 0) gl.colorname(1, 'jet') gl.colorname(2, 'jet') # gl.viewcoronal(True) #gl.view(2) #gl.orthoviewmm(0.5,0.5,0.5) #gl.savebmp('C:/Users/enzo/Downloads/Study/Current Courses/MEP/Software/mricrogl/doesthisworknow')
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.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') gl.colorfromzero(3, 1) gl.overlayload( "//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/Power2011_Dorsal_attention_mask"