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SCITRAN Scripts

Miscellaneous scripts.


oauth2cli.py

Open a browser window to get credentials for the Scitran API.

python oauth2cli.py create --auth_host_port 9000 --client-secret <client-secret> --client-id <client-id>

It creates a json file called "credentials_sdm". The credentials' access_token is also printed to stdout.

To refresh an existing token.

python oauth2cli.py refresh

To revoke an existing token.

python oauth2cli.py revoke

It is possible to pass an argument --filename to specify where the credentials are stored.

Requirements: oauth2client, httplib2


dicomsort.py

Organize a mess of dicoms into exams/series.

dicomsort.py tarsort ./mess/of/dicoms ./sort/dest ./tar/dest

The sortable dicoms will be organized into the sort destination (./sort/dest from example) by exam number and series number. Unsortable dicoms will be left in the original source directory (./mess/of/dicoms from example).

Output tarfiles will be placed into the tar destination (./tar/dest from example), and be named by their exam number and series number.


siemens_multicoil.py

Reconstruct and concatenate two niftis in the order the dicoms.tgz sources are provided on the command line. To reconstruct a Siemens multicoil scan, give the individual coil dicom.tgz as the first input, and the combined coil dicom.tgz as the second input.

siemens_multicoil.py ./path/to/individual_coils_dicoms.tgz ./path/to/combined_coils_dicoms.tgz

The output nifti will be named after the first dataset's exam and series number, suffixed with '_multicoil'i.

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