File "/home/bic/Desktop/allin/PythonScripts/skull_strip.py", line 20
    if not os.path.exists(output_dir):
                                     ^
IndentationError: unindent does not match any outer indentation level

ExceptionObject caught!

itk::ExceptionObject (0x342a3b0)
Location: "unknown" 
File: /work/jprieto/source/auto_EACSF-build/ITKv4-install/include/ITK-4.13/itkImageToImageFilter.hxx
Line: 241
Description: itk::ERROR: MaskImageFilter(0x3427ff0): Inputs do not occupy the same physical space! 
InputImage Origin: [-1.0472700e+02, 8.3143400e+01, -8.4951500e+01], InputImage_1 Origin: [-1.3292542e+02, 9.9688858e+01, 1.2550766e+02]
	Tolerance: 8.9843800e-04
InputImage Spacing: [8.9843800e-01, 8.9843800e-01, 9.0000000e-01], InputImage_1 Spacing: [9.9999994e-01, 9.9999994e-01, 1.0000000e+00]
	Tolerance: 8.9843800e-04
InputImage Direction: 1.0000000e+00 0.0000000e+00 0.0000000e+00
0.0000000e+00 -9.9844100e-01 5.5821500e-02
0.0000000e+00 5.5821500e-02 9.9844100e-01
, InputImage_1 Direction: 1.0000000e+00 0.0000000e+00 0.0000000e+00
0.0000000e+00 3.7252905e-09 -1.0000000e+00
0.0000000e+00 -1.0000000e+00 3.7252903e-09

	Tolerance: 1.0000000e-03





Traceback (most recent call last):
  File "/home/bic/Desktop/allin/PythonScripts/main_script.py", line 288, in <module>
    main(args)
  File "/home/bic/Desktop/allin/PythonScripts/main_script.py", line 156, in main
    im=itk.imread(T1_REGISTERED)
  File "/home/bic/.local/lib/python3.6/site-packages/itkExtras.py", line 641, in imread
    reader = TemplateReaderType.New(**kwargs)
  File "/home/bic/.local/lib/python3.6/site-packages/itkTemplate.py", line 469, in New
    return self._NewImageReader(itk.ImageFileReader, False, 'FileName', *args, **kwargs)
  File "/home/bic/.local/lib/python3.6/site-packages/itkTemplate.py", line 552, in _NewImageReader
    raise RuntimeError("Could not create IO object for reading file %s" % inputFileName + msg)
RuntimeError: Could not create IO object for reading file /home/bic/Desktop/allin/SkullStripping/T1_stripped.nrrd
The file doesn't exist. 
Filename = /home/bic/Desktop/allin/SkullStripping/T1_stripped.nrrd