Batch processing with Lung CT Segmenter
Use Lung CT Segmenter's batch processing function for easy sequential lung segmentation with a few mouse clicks and the following workflow:
- Check "use AI" and select an appropriate AI engine
- Uncheck "Airway segmentation", unless you use TotalSegmentator as the AI engine, because otherwise manual input would be needed
- Select the input folder
- Select the output folder
- Enable "Testmode" if required
- Disable "Testmode" if all subfolders of the input directory should be processed (this may take a long time)
- Select "Input is NIFTI" if required. In this case, NIFTI output will be generated.
- Press "Batch process"
All CT input files present in the input directory subfolders will be processed one by one. In "Testmode", only three datasets will be processed.
- Current scene will be closed
- Next CT dataset will be loaded
- Lung segmentation will be performed
- Segmentation results will be saved to the output folder
- Execution times will be measured.
3D Slicer will be not responsive until the operation has finished. This may take hours. If you need to cancel the process please press the cancel button a few times.
Progress can be monitored in the Python Console or the Status Message region:
The structure of the input folder should contain one immediate subdirectory for each dataset. In each subdirectory, either a "CT.nrrd" file or a "ct.nii.gz" file must be present. CT input files that are placed into the input folder directly (without subdirectories) will be ignored.
The structure of the input folder will be mirrored to the output folder during processing.
The content of an output subfolder of the output folder could look like this ("Input is NIFTI" was checked):
