bcn-medtech / bcn-medtech/reImagineClient
Anonimization fails if the original directory has a space in the name
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Description
I get this error during anonimisation. File name is
ADUHEART429_TWOCHAMBER_1.MR.0027.0001.2017.11.17.16.30.17.827150.3253495.IMA
in folder:
/Users/gbernardino/Data/aduheartultimos/aduheart231/2 chamber'
Could it be that there are spaces in the path?
> An error occurred during anonimization!
> Reason: Error while running anonimization: undefined Command failed: /Applications/reImagineClient.app/Contents/Resources/scripts/runDeid.sh /Users/gbernardino/Data/aduheartultimos/aduheart231/2 chamber /Users/gbernardino/Documents/reimagine/an/63e69fdf-a8ef-4d80-a5f9-3ca276b79556 /Applications/reImagineClient.app/Contents/Resources/scripts/deiden/src/deidTest_pyd.py /Users/gbernardino/Documents/reimagine/patients.sqlite /Users/gbernardino/miniconda3/bin/activate /Applications/reImagineClient.app/Contents/Resources/scripts/deiden/src/deid_light.dicom /Users/gbernardino/Documents/reimagine/patients.csv /Users/gbernardino/Documents/reimagine/headers
> activate does not accept more than one argument:
> ['/Users/gbernardino/Data/aduheartultimos/aduheart231/2 chamber', '/Users/gbernardino/Documents/reimagine/an/63e69fdf-a8ef-4d80-a5f9-3ca276b79556', '/Applications/reImagineClient.app/Contents/Resources/scripts/deiden/src/deidTest_pyd.py', '/Users/gbernardino/Documents/reimagine/patients.sqlite', '/Users/gbernardino/miniconda3/bin/activate', '/Applications/reImagineClient.app/Contents/Resources/scripts/deiden/src/deid_light.dicom', '/Users/gbernardino/Documents/reimagine/patients.csv', '/Users/gbernardino/Documents/reimagine/headers']
>
> /Applications/reImagineClient.app/Contents/Resources/scripts/runDeid.sh: line 15: pushd: scripts/deiden/: No such file or directory
> usage: deidTest_pyd.py [-h] [--outdir OUTDIR] [--recipe RECIPE]
> [--save-headers] [--headers-dir HEADERS_DIR]
> [--db-location DB_LOCATION]
> [--export-on-save EXPORT_ON_SAVE]
> basedir
> deidTest_pyd.py: error: unrecognized arguments: chamber
>
> Check into the logs for additional informations
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