vxdSort.py

Synopsis

Sort DICOM files into patient/study/series hierarchy, and convert to NIFTI. This module also provides anonymization options for the sorted DICOM files.

Usage

vxdSort.py -i/--input <source DICOM folder> [options]

Use either -i or --input to specify the path to the source folder, containing the DICOM files

Description

If no additional options are passed, this program will sort all DICOM files present in the source DICOM folder into a hierarchical structure.

The output is written to a new subfolder, within the source DICOM folder root. The name of the output folder is specified in the config.json file (see Setting the Configuration Parameters; the default is vxd_dicom). By default, the output follows the format shown below. If multiple patients are present in the source DICOM folder, a new patient folder will be created for each.

- patient name
--- study date <yyyymmdd>
------ series 01
------ series 02, etc...

Options

-n / --nifti Flag to create a mirrored copy of the sorted DICOM files, in NIFTI format. A new parent folder will be created (default folder name is vxd_nifti). The file structure within this will match that used for the sorted DICOM files, with a compressed NIFTI file being stored in each series subfolder. Series with a SeriesDesciption DICOM tag listed in the config[‘excludeNifti’] dictionary entry will not be converted to NIFTI (see Setting the Configuration Parameters). An additional JSON sidecar file will be written, containing a summary of some key DICOM tags.
-a / --anon Flag to anonymize the DICOM files as they are sorted. The recipe file stored in $VXD_HOME/vxdSort/deid_voxelDesk.dicom will be used to determine which DICOM tags should be removed or updated. This recipe file can be edited - see Setting the Configuration Parameters).

By default, the patient names in the source DICOM folder will be replaced by vxdAnon-0000, vxdAnon-0001, etc, however, this can be changed using the --codes option described below.
-c / --codes ‘list of patient codes’. Replaces the PatientName and PatientID DICOM tags in the anonymized files with a user-supplied patient code. Supply one code for each patient present in the source DICOM folder, using a comma-separated list.

Example Usages

Sort the DICOM files stored in the myDICOMs folder into patient/study/series folders:
```
vxdSort.py --input myDICOMs
```
This will create a new folder called myDICOMs/vxd_dicom, containing the sorted DICOM files.
Sort the DICOM files stored in the myDICOMs folder, and create NIFTI versions of each series
```
vxdSort.py --input myDICOMs --nifti
```
This will create two new folders: myDICOMs/vxd_dicom for the sorted DICOMS, and myDICOMs/vxd_nifti for the NIFTIs.
Sort the DICOM files stored in the myDICOMs folder, and anonymize the sorted files
```
vxdSort.py --input myDICOMs --anon
```
This will create a new folder called myDICOMs/vxd_dicom, containing the sorted DICOM files. As the --codes option has not been used, each patient in the myDICOMs folder will be renamed as vxdAnon-0000, vxdAnon-0001, etc.
Sort the DICOM files stored in the myDICOMs folder, anonymize the sorted files with user-supplied patient codes, and convert to NIFTI
```
vxdSort.py --input <source DICOM folder> --anon --codes 'Patient-001, Patient-002' --nifti
```
This will create two new folders: myDICOMs/vxd_dicom for the sorted DICOMS, and myDICOMs/vxd_nifti for the NIFTIs. The patient folders will be named myDICOMs/vxd_dicom/Patient-001 and myDICOMs/vxd_dicom/Patient-002.