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Volume sequence registration for 3D Slicer

This extension registers a sequence of volumes (3D+t a.k.a. 4D image data) to a selected volume. Processing results is a transform sequence (3D displacement field changing in time) and motion-compensated volume sequence. The transform sequence can be used for deforming point targets or structures.

Applications include motion-compensation for volume comparison and analysis of organ motion.

The module uses Elastix registration toolkit through SlicerElastix extension.

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See full result here (animated gif; top row: before registration, bottom row: motion-compensated output):


Simple example

  1. Load sample 4D cardiac sequence by opening SampleData module and clicking on CTPCardio data set. The sequence browser toolbar will appear that can be used to play/pause/browse the volume sequence.

  2. Perform registration

  • Switch to Sequence registration module (in Sequences category in the module list)
  • Input volume sequence: CTP-cardio
  • Output volume sequence: Create new sequence
  • Output transform sequence: Create new sequence
  • Advanced section / Fixed frame at timepoint: 7 (the first frame does not contain contrast agent, so registering all the contrasted frames to it would not provide optimal results)
  • Click Register -- and wait about 10 minutes
  1. Review results
  • After the registration is completed, the motion-compensated output volume sequence is shown in slice viewers.
  • Use the sequence browser toolbar to replay the sequence.
  • Transform can be visualized by switching to Transforms module, selecting the output transform, and adjusting options in Display section.

How to register your own data

All the required input is a volume sequence node in Slicer. In the future, the module will support specifying masks for specifying a region of interest for registration.

Create volume sequence from 4D DICOM image:

  1. Load up the DICOM Browser in Slicer

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  1. Make sure the Advanced checkbox is checked, and the MultiVolumeImporterPlugin is also checked

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  1. Import your dataset

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  1. Select your dataset and click Examine

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  1. Select the one with the reader MultiVolume and click Load

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  1. Click the Save button in the top pane of Slicer

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  1. Check the MultiVolume that was chosen in step 5 and choose a folder to save it in

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  1. Edit the file name by double-clicking on it, and append .seq to the end of the filename (when you load this image into Slicer later, this .seq.nrrd file extension gives a hint to Slicer that the file should be interpreted as a volume sequence)

  2. Click Save

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  1. Close the Scene by clicking File -> Close Scene

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  1. Click the Data button at the top of Slicer

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  1. Choose the file you saved in step 8 and click Open, then click Ok to load the MultiVolume Sequence

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  1. Now you can choose the sequence as input in the Sequence Registration Module

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Create volume sequence from 4D NRRD image:

  • Perform steps 8-13 above

Create volume sequence from many scalar volumes

  1. Open the Sequences module

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  1. Create a new Sequence

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  1. Add scalar volumes by selecting them and clicking the green left arrow

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