Hello,

I am using the most recent update of the Auto_EACSF software (1.7.4-Linux) and am getting "Could not create IO object for reading file..." for various files (see attached error & output logs). The coronal_mask_70 output file is blank when i try to view it. There is no new_FINAL_QCistern.nrrd file in the output directory either. I am providing my own T1 (nrrd), brainmask (nrrd), and tissue segmentation (mha). Any help would be greatly appreciated!

Thanks!
Alex

output_log attached

Hi Alex, 

The release 1.7.5 fixes this bug. Since you were providing a brainmask, the directory 'SkullStripping' was not created. 

Please let me know if you find any other issue. 

Best,

Thanks Juan!

I just tried using the newest version and ran into the following error:

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


Attached is the error_log and output_log.

Thanks again!

-Alex

outputlog

I updated version 1.7.5 with the fix for this indentation error. 

Please let me know how it goes. 

Best,

Hi Juan,

I used the newest version but am still running into a few errors.  I am still getting "Could not create IO object for reading file..." for files in the finalmasking directory (see attached error log). Also, I did not get a final new_FINAL_QCistern.nrrd output file. Maybe my input files aren't proper?

PS - Using this version I do now have a skullstripping directory in the output directory.

Best,
Alex

outputlog

Apologies, the error log i most recently attached was from an older version. Now attached is the most recent error log.

Hello, 
Since you are providing a mask image, could you make sure that the input mask is in the same space as your T1 image? 
This error is raised when the images do not occupy the same physical space. Maybe there is a transformation that needs to be applied to your mask image. 

ExceptionObject caught!

itk::ExceptionObject (0x1c00f90)
Location: "unknown"
File: /work/jprieto/source/auto_EACSF-build/ITKv4-install/include/ITK-4.13/itkImageToImageFilter.hxx
Line: 241
Description: itk::ERROR: MaskImageFilter(0x1c03ff0): 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