help > tissue_seg_script errors
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Oct 31, 2019  07:10 PM | petemade
tissue_seg_script errors
Hi,

We've been attempting to run images through Auto_EACSF but have encountered some issues when the images hit the tissue_seg_script.py. It appears as if the template_to_T1_Warp.nii.gz and template_to_T1_Affine.nii.gz files aren't being created (see output below), which Auto_EACSF subsequently can't find. We are using v1.4.1_RHL6 on Linux Red Hat 7 with python 3 and itk 5.0.1.

>>> tissue_seg_script.py : Running: /compute/research_bin/antsbin/bin/WarpImageMultiTransform 3 /software/Auto_EACSF_Pipeline/pediatric-atlas-1year-T1-ABC/DeepGray5Class/stripped/template.mha /HCP_images/output/144226/TissueSegAtlas/template.mha /HCP_images/output/144226/TissueSegAtlas/template_to_T1_Warp.nii.gz /HCP_images/output/144226/TissueSegAtlas/template_to_T1_Affine.txt -R /HCP_images/output/144226/SkullStripping/144226_T1_stripped.nrrd

FIELD: /HCP_images/output/144226/TissueSegAtlas/template_to_T1_Warp.nii.gz
AFFINE: /HCP_images/output/144226/TissueSegAtlas/template_to_T1_Affine.txt
moving_image_filename: /software/Auto_EACSF_Pipeline/pediatric-atlas-1year-T1-ABC/DeepGray5Class/stripped/template.mha components 1
output_image_filename: /HCP_images/output/144226/TissueSegAtlas/template.mha
reference_image_filename: /HCP_images/output/144226/SkullStripping/144226_T1_stripped.nrrd
[0/2]: FIELD: /HCP_images/output/144226/TissueSegAtlas/template_to_T1_Warp.nii.gz
[1/2]: AFFINE: /HCP_images/output/144226/TissueSegAtlas/template_to_T1_Affine.txt
User Linear interpolation
Exception caught during WarpImageMultiTransform.

itk::ImageFileReaderException (0x350a890)
Location: "unknown"
File: /compute/research_bin/antsbin/ITKv5-install/include/ITK-5.0/itkImageFileReader.hxx
Line: 142
Description: Could not create IO object for reading file /HCP_images/output/144226/TissueSegAtlas/template_to_T1_Warp.nii.gz
The file doesn't exist.
Filename = /HCP_images/output/144226/TissueSegAtlas/template_to_T1_Warp.nii.gz

Any ideas as to why it's not generating the files?

Thanks,
Maddy
Nov 8, 2019  05:11 PM | petemade
RE: tissue_seg_script errors
I've got the solution! For future users, it turns out that this was a library issue. The solution was installing libhistory.so.5 and exporting LD_LIBRARY_PATH to this lib's location. 

-Maddy
Nov 11, 2019  06:11 AM | Martin Styner
RE: tissue_seg_script errors
Great, that means some of tools previously did not run (because a system library was missing, the library history.so.5 is a system library that is expected by several tools to be present if you use the precompiled versions). 

One way to solve this is how Maddy did it. Another way would be to find an rpm for your system that contains that library and install that rpm, and a third would be to compile it locally on your system.

Martin
Originally posted by petemade:
I've got the solution! For future users, it turns out that this was a library issue. The solution was installing libhistory.so.5 and exporting LD_LIBRARY_PATH to this lib's location. 

-Maddy