'//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']
#YA_filename = ['//cifs.rc.ufl.edu/ufrc/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/Level2_Results/MRI_files/05_MotorImagery/youngadult/spmT_0004.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_0005.nii']
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()
gl.backcolor(255, 255, 255)
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1, 50)
#open overlay: show negative regions
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname(2, "3blue")
gl.colorbarposition(0)
#"a"xial, "c"oronal and "s"agittal "r"enderings
gl.mosaic("A R 0 C R 0 S R 0; A R -0 C R -0 S R -0")
gl.loadimage(
'//exasmb.rc.ufl.edu/blue/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/MNI_2mm.nii'
)
# gl.loadimage('//exasmb.rc.ufl.edu/blue/rachaelseidler/tfettrow/Crunch_Code/MR_Templates/SUIT_Nobrainstem_2mm.nii')
# gl.loadimage('//exasmb.rc.ufl.edu/blue/rachaelseidler/tfettrow/Crunch_Code/spm_TF/spm12/toolbox/suit/atlas/Cerebellum-SUIT-maxprob.nii')
gl.opacity(1, 10)
######################################
# rois_plotted=1;
# this_index=0;
for this_network in networks_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.overlayload(
"//exasmb.rc.ufl.edu/blue/rachaelseidler/share/FromExternal/Research_Projects_UF/CRUNCH/MiM_Data/ROIs/"
+ this_network)
#gl.minmax(1,.01,.01)
#gl.minmax(2,.01,.01)
#gl.minmax(3,.01,.01)
#gl.minmax(4,.01,.01)
#gl.minmax(5,.01,.01)
#gl.minmax(6,.01,.01)
#gl.minmax(7,.01,.05)
#gl.minmax(8,.01,1)
#gl.minmax(9,.02,.025)
import gl
gl.resetdefaults()
gl.loadimage('spm152')
gl.backcolor(255, 255, 255)
gl.mosaic("S R -0");
import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1, 50)
#open overlay: show negative regions
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname(2, "3blue")
gl.mosaic("A L+ H -0.2 -24 -16 16 40; 48 56 S X R 0")