Skip to content

Anonimization fails if the original directory has a space in the name #29

Description

@gbernardino

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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions