def main():
EXP_DIR='results/graph_neural_mapping'
NII_DIR='saliency_nii'
SAVE_DIR='saliency_img'
os.makedirs(os.path.join(EXP_DIR, SAVE_DIR), exist_ok=True)
gl.resetdefaults()
gl.loadimage('mni152')
gl.overlayloadsmooth(True)
gl.opacity(0, 50)
gl.colorbarposition(0)
visualize_axial(os.path.join(EXP_DIR, NII_DIR), os.path.join(EXP_DIR, SAVE_DIR))
visualize_sagittal(os.path.join(EXP_DIR, NII_DIR), os.path.join(EXP_DIR, SAVE_DIR))
visualize_colorbar(os.path.join(EXP_DIR, SAVE_DIR))
gl.resetdefaults()
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
#Conceptual Fig
import gl
import sys
print(sys.version)
print(gl.version())
gl.resetdefaults()
gl.loadimage(
'//cifs.rc.ufl.edu/ufrc/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/Template_4_IXI555_MNI152_GS.nii'
)
# OAc_filenames=['C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/OAc_Flat', \
# 'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/OAc_Low', \
# 'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/OAc_Med', \
# 'C:/Users/tfettrow/Dropbox (UFL)/CrunchReview/Tables_and_Figs/OAc_Hard' ]
# for this_index in range(0,len(OAc_filenames)):
# gl.overlaycloseall()
# gl.overlayload(OAc_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(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' ]
import gl
gl.resetdefaults()
gl.loadimage('/Users/chris/src/dcm_qa/Ref/fMRI_MB_asc_25.nii')
#gl.opacity(1,5)
#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)
@author: Bryce
--- deSCRIPTION ---
"""
# Testing - run this from 00_Multiple_files directory
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')
import gl
gl.resetdefaults()
gl.loadimage('chris_t2')
gl.orthoviewmm(0, 50, 0)
gl.minmax(0, 2, 155)
gl.backcolor(255, 255, 255)
gl.invertcolor(0, 1)
#This MatCap looks nice for Rendering
#gl.shadermatcap('Cortex')
#gl.clipazimuthelevation(0.5, 0, 90)
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()
#the desai atlas comes with AFNI
# if this fails, use File/OpenAFNI to set AFNI folder
# gl.loadimage(pth+'stats.FT+orig.HEAD')
#gl.loadimage('TTatlas+tlrc.HEAD')
gl.resetdefaults()
gl.orthoviewmm(0, 0, 0)
#gl.loadimage('TTatlas+tlrc')
gl.loadimage('/Users/chris/src/AICHAlr')
#gl.generateclusters(0)
#gl.generateclusters(0, 0.5, 32, 1, 0)
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
gl.resetdefaults()
gl.orthoviewmm(0, 0, 0)
gl.loadimage('/Users/chris/V1.nii.gz')
#gl.loadimage('/Users/chris/FA.nii.gz')
#open overlay: show positive regions
#gl.overlayload('/Users/chris/V1.nii.gz')
#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)
import gl
gl.resetdefaults()
ktime = 30
ksteps = 72
gl.resetdefaults()
gl.loadimage('CT_Abdo')
#adjust contrast to show bones
gl.minmax(0, -1024, 640)
for x in range(1, ksteps):
gl.azimuthelevation(160 + (x * 5), 30)
gl.wait(ktime)
#adjust color scheme to show kidneys
gl.colorname(0, 'CT_Kidneys')
gl.shadername('Tomography')
#gl.shaderadjust('brighten', 1.2)
for x in range(1, ksteps):
gl.azimuthelevation(160 + (x * 5), 30)
gl.wait(ktime)
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.resetdefaults()
gl.loadimage('chris_MRA')
#load Maximum Intensity Projection Shader
gl.shadername('MIP')
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')
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
import sys
import random
print(sys.version)
print(gl.version())
gl.resetdefaults()
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
import gl
gl.resetdefaults()
#the desai atlas comes with AFNI
# if this fails, use File/OpenAFNI to set AFNI folder
gl.loadimage(
'/Users/chris/tmp/atlases/HarvardOxford-cort-maxprob-thr0-1mm.nii.gz')
#gl.overlayload(pth+'ttest.wav.t0.p3.RT_REML.L-A.allmask+tlrc.HEAD')
#Conceptual Fig
import gl
import sys
print(sys.version)
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'
import gl
gl.resetdefaults()
gl.loadimage('/Users/chris/Neuro/MRIcroGLold/templates/inia19-NeuroMaps.nii.gz')
gl.scriptformvisible(1)
gl.atlashide(0)
gl.atlasshow(0, 151,153,129)
gl.atlasshow(0, 1215,1,3,7)
print('Regions '+ str(gl.atlasmaxindex(0)) )
#print(gl.atlaslabels(0))
# %% Libraries ----------------------
import gl
import os
# %% General----------------------
#gl.resetdefaults()
gl.backcolor(255, 255, 255)
# %% background image ----------------------
gl.loadimage('mni152')
# %% 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)
overlay_path = data_path + '/' + subject + '/allen_annotation_invsynned_to_' + subject + '_adjusted_cerebellum_lobular_mc_si.nii.gz'
output_path = analysis_path + '/' + subject + '_50rot_overlay_si_si'
print(input_path)
print(overlay_path)
for j in range(2):
if j == 1:
output_path = output_path + '_cutout'
output_gif_path = output_path + '.gif'
print(output_path)
if not os.path.exists(output_path):
os.mkdir(output_path)
gl.loadimage(input_path)
if i == 3: # load both subcortical and cerebellum
gl.overlayload(overlay_path)
gl.overlayload(overlay2_path)
gl.opacity(1, 40)
gl.opacity(2, 70)
gl.minmax(1, 0, 1243)
gl.minmax(2, 0, 1243)
gl.colorname(1, 'x_rain')
gl.colorname(2, 'x_rain')
#gl.fullscreen(0)
else:
gl.overlayload(overlay_path)
gl.opacity(1, 40)
gl.minmax(1, 0, 1243)
