Does Slicer support the batch processing?

[glhfgg1024]

Operating system: Windows 10
Slicer version: 4.8.0
Expected behavior: batch processing
Actual behavior: Not sure

Hi there,

I’m on these things: first import the DICOM files into Slicer, then for each patient, I need to save the PET/CT and the RT Structure Set to Nifti format for subsequent processing. Current I need to handle this data case by case. I was wondering if the Slicer can support the batch processing. After we defined a pipeline based on Slicer and the extensions, the batch processing module could repeat the processing automatically and also could record the cases with failure.

Thanks.

[cpinter (Csaba Pinter)]

Hello,

This question has been asked many times in the mailing list, for example

RTstruct to Label map

Hi, I have 200 dicom datapoints that contain a image and a RTstruct for the segmentations. I need to convert all RTstructs to Label volumes (maps) and can do this with the segmentations module. However, I have to perform every step manually and I am thus looking for a way to do it batch-wise. Since the segmentations module does not have a CLI, I was wondering if there is another solution that would allow me to access the module without the GUI. Best regards, Alain

and

Slicer batch processing question (--no-main-window --python-script)

Hi everyone, I am trying to find the best way to quickly batch process a number of folders containing head MRI dicom files to .nii files. Basically the pipeline should work like this: import the dicom files > load them as a volume > save the volume as a .nii file. I am trying to do this using the slicer from terminal: Slicer --no-main-window --python-script (as is described in here https://www.slicer.org/wiki/Documentation/Nightly/Developers/Python_scripting#How_to_access_a_scripted_module_fro…

I hope this helps.

[pieper (Steve Pieper (Isomics, Inc.))]

Also you can have a look at the CaseIterator extension. It is currently geared for interactive work, but it would be great to see it extended to also work with batch pipelines.

GitHub - JoostJM/SlicerCaseIterator: Simple Scripted Module to batch process...

https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SlicerCaseIterator

[glhfgg1024]

Hi @cpinter and @pieper, thank you very much for your kind reply and suggestions! Very helpful!

[timeanddoctor (Li Zhenzhu)]

I installed SlicerCaseIterator and was confused by this wiki. The .csv table should be created including the dir of all volume and segment before load them? Can I save/write a loaded volume and mask segmentation in slicer by this module? I tried to do that but nothing happen even clicking the batch buttom for an empty table.