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autopipeline failure to save RTStruct due to name containing invalid character "<" #45

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jpeoples opened this issue Jul 19, 2022 · 2 comments
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autopipeline failure to save RTStruct due to name containing invalid character "<" #45

jpeoples opened this issue Jul 19, 2022 · 2 comments

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@jpeoples
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jpeoples commented Jul 19, 2022 •
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I ran the autopipeline again to process our RTSTRUCTs. This mostly works. There were a couple small issues.

The first is, as I said in the title, one of the RTStruct contours contains "<", which creates an error. I believe this is most likely because "<" is invalid in a Windows path.

The error text is simply

** ERROR (nifti_image_write_hdr_img2): cannot open output file 'liver_autopipe/0_20243743626/RTSTRUCT_CT/z_liver<1500.nii.gz'

The other errors were a couple warnings about being unable to get points for a few ROIs in one of the subjects, but I think they might just be empty.
@skim2257
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To implement file path checking with these invalid characters: https://stackoverflow.com/a/31976060/15664287

skim2257 added a commit that referenced this issue Oct 25, 2022
@skim2257
New flags: --update, --roi_select_first, --roi_separate, better mask_…
89b715b 
…label parsing (#45)

* added --update flag, needs test.

* Added --roi_select_first and --roi_separate flags for advanced ROI parsing for contours.

* mask_label parsing for illegal Windows/Unix characters (Issue #45 resolved)
@skim2257
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Resolved with commit.

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@jpeoples @skim2257