plastimatch command returned non-zero exit status 1

[peterwu19881230]

Hi, dear developers:

When I was opening the following notebook in colab, I wasn't able to get the final image viewer as expected:
https://github.com/ImagingDataCommons/IDC-Examples/blob/master/notebooks/cohort_preparation.ipynb

May I get some help from here? Thanks!

The error message (about plastimatch package) :

Running 'plastimatch convert' with the specified arguments:
--input tutorial/data/dicom/LUNG3-81/CT
--output-img tutorial/data/processed/nrrd/LUNG3-81/LUNG3-81_ct.nrrd
Command '['plastimatch', 'convert', '--input', 'tutorial/data/dicom/LUNG3-81/CT', '--output-img', 'tutorial/data/processed/nrrd/LUNG3-81/LUNG3-81_ct.nrrd']' returned non-zero exit status 1.

Running 'plastimatch convert' with the specified arguments:
--input tutorial/data/dicom/LUNG3-81/RTSTRUCT
--referenced-ct tutorial/data/dicom/LUNG3-81/CT
--output-prefix tutorial/data/processed/nrrd/LUNG3-81/RTSTRUCT
--prefix-format nrrd
--output-ss-list tutorial/data/processed/nrrd/LUNG3-81/RTSTRUCT_content
Command '['plastimatch', 'convert', '--input', 'tutorial/data/dicom/LUNG3-81/RTSTRUCT', '--referenced-ct', 'tutorial/data/dicom/LUNG3-81/CT', '--output-prefix', 'tutorial/data/processed/nrrd/LUNG3-81/RTSTRUCT', '--prefix-format', 'nrrd', '--output-ss-list', 'tutorial/data/processed/nrrd/LUNG3-81/RTSTRUCT_content']' returned non-zero exit status 1.

Running 'plastimatch convert' with the specified arguments:
--input tutorial/data/dicom/LUNG3-81/CT
--output-img tutorial/data/processed/nii/LUNG3-81/LUNG3-81_ct.nii.gz
Command '['plastimatch', 'convert', '--input', 'tutorial/data/dicom/LUNG3-81/CT', '--output-img', 'tutorial/data/processed/nii/LUNG3-81/LUNG3-81_ct.nii.gz']' returned non-zero exit status 1.

[wlongabaugh]

@denbonte would you be able to provide info on this?

[denbonte]

Dear @peterwu19881230 - sorry for the delayed response!

I checked the Cohort Preparation Colab notebook, and everything works fine on my side. I ran it once "as it was", and then updated the notebook to include the packaged version of PyPlastimatch (instead of cloning the repository as before - nothing really changes besides the notebook being a bit cleaner).

Could you please provide us with some more details so that we can help fixing the problem?

Running 'plastimatch convert' with the specified arguments:
--input tutorial/data/dicom/LUNG3-81/CT
--output-img tutorial/data/processed/nrrd/LUNG3-81/LUNG3-81_ct.nrrd
Command '['plastimatch', 'convert', '--input', 'tutorial/data/dicom/LUNG3-81/CT', '--output-img', 'tutorial/data/processed/nrrd/LUNG3-81/LUNG3-81_ct.nrrd']' returned non-zero exit status 1.

Running 'plastimatch convert' with the specified arguments:
--input tutorial/data/dicom/LUNG3-81/RTSTRUCT
--referenced-ct tutorial/data/dicom/LUNG3-81/CT
--output-prefix tutorial/data/processed/nrrd/LUNG3-81/RTSTRUCT
--prefix-format nrrd
--output-ss-list tutorial/data/processed/nrrd/LUNG3-81/RTSTRUCT_content
Command '['plastimatch', 'convert', '--input', 'tutorial/data/dicom/LUNG3-81/RTSTRUCT', '--referenced-ct', 'tutorial/data/dicom/LUNG3-81/CT', '--output-prefix', 'tutorial/data/processed/nrrd/LUNG3-81/RTSTRUCT', '--prefix-format', 'nrrd', '--output-ss-list', 'tutorial/data/processed/nrrd/LUNG3-81/RTSTRUCT_content']' returned non-zero exit status 1.

Running 'plastimatch convert' with the specified arguments:
--input tutorial/data/dicom/LUNG3-81/CT
--output-img tutorial/data/processed/nii/LUNG3-81/LUNG3-81_ct.nii.gz
Command '['plastimatch', 'convert', '--input', 'tutorial/data/dicom/LUNG3-81/CT', '--output-img', 'tutorial/data/processed/nii/LUNG3-81/LUNG3-81_ct.nii.gz']' returned non-zero exit status 1.

Could you, for instance, share the cohort you run the notebook on?

About that - and if that is the problem - please, remember you need to generate a cohort from IDC before running the notebook (and create a Google Cloud project to run the BigQuery), and then populate the two following cells accordingly.

In the second case, you'll need to insert only the BQ Table ID - as the project ID is set automatically (from the variable initialised at the other cell).

If you need help with those two steps, we will be happy to provide you some - so don't hesitate asking! 😄

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I'm attaching a couple of screenshots of my run: