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)
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
print(count)
gl.orthoviewmm(0, y, -4)
gl.view(2)
gl.linewidth(0)
gl.colorbarposition(0)
filepath = os.path.join(output_dir_path, 'imagenew' + '_' +
str(round(count)).rjust(3, '0')) + '_' + str(y)
gl.savebmp(filepath)
y = y + y_step
gl.colorname(2, '3blue') gl.colorname(3, '1red') gl.colorname(4, '3blue') output_dir_path = os.path.join(analysis_path, 'imageSequenceFolders', 'aFD_InDe') if not os.path.exists(output_dir_path): os.mkdir(output_dir_path) y_min = -120 y_max = 90 y_step = 1 y = y_min count = 0 while y <= y_max: print(y) count = count + 1 print(count) gl.orthoviewmm(-3, y, -14) gl.view(2) gl.linewidth(0) gl.colorbarposition(0) filepath = os.path.join(output_dir_path, 'imagenew' + '_' + str(round(count)).rjust(3, '0')) + '_' + str(y) gl.savebmp(filepath) y = y + y_step
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 count = 0 while y <= y_max: print(y) count = count + 1 print(count) gl.orthoviewmm(0, y, 0) # why at first (-3, y, -14)? gl.view(2) gl.linewidth(0) gl.colorbarposition(0) filepath = os.path.join(output_dir_path, 'imagenew' + '_' + str(round(count)).rjust(3, '0')) + '_' + str(y) gl.savebmp(filepath) y = y + y_step
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.orthoviewmm(37, -14, 47)