help > tissue_seg_script errors
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

Threaded View

TitleAuthorDate
tissue_seg_script errors
petemade Oct 31, 2019
petemade Nov 8, 2019
Martin Styner Nov 11, 2019