PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG script

Script to convert NIFTI Predictions ( as output from the model inference ), back into the original DICOM context ( as SEG modalities ). The NIFTI Predictions are converted into DICOM SEG and assigned to the corresponding original DICOM Study.

usage: PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG [-h] --data-folder
                                                     DATA_FOLDER
                                                     --dicom-folder
                                                     DICOM_FOLDER
                                                     --output-folder
                                                     OUTPUT_FOLDER
                                                     --pred-suffix PRED_SUFFIX
                                                     [--n-workers N_WORKERS]
                                                     --template-file
                                                     TEMPLATE_FILE
                                                     --study-id-summary
                                                     STUDY_ID_SUMMARY
                                                     [-v | -q]

Named Arguments

--data-folder

Data Folder containing the NIFTI Predictions.

--dicom-folder

DICOM Folder containing the original Data.

--output-folder

Folder where to store the generated DICOM SEG.

--pred-suffix

Suffix to append to the Patient folder name to identify the NIFTI prediction.

--n-workers

Number of Parallel Threads.

Default: '1'

--template-file

DCMQI DICOM SEG Template, generated from http://qiicr.org/dcmqi/#/seg

--study-id-summary

Study ID Summary, generated when converting the DICOM Dataset to a NIFTI Dataset.

-v, --verbose

Enable verbose output in terminal. Add multiple times to increase verbosity.

-q, --silent

Suppress most log outputs in terminal.

Example call:

PyMAIA_convert_NIFTI_predictions_to_DICOM_SEG --data-folder <NIFTI_DATA_FOLDER> --dicom-folder <DICOM_DATA_FOLDER> --output-folder <DICOM_SEG_FOLDER> --pred-suffix _seg.nii.gz --template-file <DCMQI_TEMPLATE> --study-id-summary STUDY_ID_DICT.json