Setting the Configuration Parameters

The global parameter settings for voxelDesk are stored in the config.json file, which resides in the $VXD_HOME/vxdSetup folder.

The voxelDesk installation comes with a default config.json file. To make changes to any of the default parameter settings, first open the $VXD_HOME/writeConfigFile.py python script, in your favourite editor.

All configuration parameters are held in a Python dictionary called config, entries from which are written to the config.json file. Values for different keys in the dictionary can be set by editing the entries in the $VXD_HOME/writeConfigFile.py python script.

Following this, the config.json file must be updated. This can be done by running the writeConfigFile function from a terminal window, i.e.

writeConfigFile.py

An explanation of the keys used in the config dictionary is given below:

  • config['sortedDicomFolderName'] = folder name used to store sorted DICOM files (default: vxd_dicom)

  • config['sortedNiftiFolderName'] = folder name used to store sorted NIFTI files (default: vxd_nifti)

  • config['defaultTargetPattern'] = string defining the output file and directory names based on the DICOM tags in the file. The default is:

/%PatientName/%StudyDate/%SeriesNumber-%SeriesDescription/%SeriesDescription-%InstanceNumber.dcm'

which will tell voxelDesk to sort DICOM files into the following file structure:

- PatientName
--- 20211110 <study date in yyyymmdd format>
------ 001-t2_tse_tra_2mm <series number-series description>
--------- t2_tse_tra_2mm-001.dcm <series description-instance number>
--------- t2_tse_tra_2mm-002.dcm etc...

  • config['excludeNifti'] = list of series descriptions to skip in the conversion between DICOM and NIFTI. Some DICOM series, such as 3-plane localizers and diffusion tensor DICOM files, do not convert reliably to NIFTI format (default ['localizer', 'survey', 'phoenix', 'iso_tensor'])

  • config['deidRecipe'] = The name of the deid receipe file used to anonymize DICOMs (default: deid_voxelDesk.dicom). This file must reside in the $VXD_HOME/vxdSort folder. If you would like to customize the anonymization procedure, information on how to use deid recipe files can be found here.

Warning

The anonymization provided by voxelDesk software is issued with no guarantees or warranty. Always check the anonymization requirements of your local ethics committee or IRB.