Documentation/Nightly/Modules/MultiVolumeImporter

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Introduction and Acknowledgements

This work is supported by NA-MIC, NAC, NCIGT, and the Slicer Community. This work is partially supported by the following grants: P41EB015898, P41RR019703, R01CA111288 and U01CA151261. Author: Andrey Fedorov, Jean-Cristophe Fillion Robin, Julien Finet, Steve Pieper, Ron Kikinis Contact: Andrey Fedorov <email>fedorov@bwh.harvard.edu</email>

National Center for Image Guided Therapy (NCIGT)   National Alliance for Medical Image Computing (NA-MIC)   Surgical Planning Laboratory (SPL)   Kitware, Inc.   Neuroimage Analysis Center (NAC)

Module Description

This module provides support for importing multivolume (multiframe) data.

Use Cases

Most frequently used for these scenarios:

• importing multiple frames defined in the same coordinate frame, saved as individual volumes in NRRD, NIfTI, or any other image format supported by 3D Slicer
• for the multi-frame data stored in DICOM format, DICOM module should be used instead; the data should be automatically recognized while parsing the dataset in DICOM module.

Tutorials

• Sample datasets are available:
  • File:Cardiac ECGg CT.tgz (ECG-gated contrast-enhanced cardiac CT). Short movie

Panels and their use

Basic settings Input directory: location of the input data as a collection of frames. Frames can be in independent volume files or a single 4D NIfTI file with the selected directory. IMPORTANT If you use User-defined non-DICOM input data type, the frames will be sorted based on the alphanumerical order of the frame filenames. If you have more than 10 frames, you should name them as follows to make sure they are ordered correctly. Correct naming: frame001.nrrd, frame002.nrrd, ..., frame023.nrrd, ..., frame912.nrrd Incorrect naming: frame1.nrrd, frame2.nrrd, ..., frame14.nrrd, ..., frame1045.nrrrd. The only files contained in the directory from which you are trying to import should be image volumes. The module will attempt to read each of these files! Output node: MultiVolume node that will keep the loaded data. You need to create a new node or select and existing one when importing the data.

Settings panel

• Advanced settings: contains elements that can be changed by the user. These items will be associated with the resulting multivolume, and will be available in case they are needed for the subsequent post-processing of the data (e.g., for pharmacokinetic modeling)
  • DICOM tag: in all modes, shows the DICOM tag that will be used to separate individual frames/volumes in the DICOM series. This field does not have meaning when the input data type is non-DICOM!
  • Frame identifying units: automatically populated for pre-defined tags. Needs to be defined for other input data types.
  • Initial value: values of the frame-identifying units for non-DICOM data type.

• Import button: once the panels are populated with the appropriate settings, hit this button to import the dataset into Slicer. Note that depending on the size of the data this operation can take significant time, so be patient!

Related Modules

Once the multivolume dataset is loaded, it can be viewed and further explored using MultiVolumeExplorer module.

Documentation/Nightly/Modules/PkModeling extension can be used for pharmacokinetic analysis of the DCE MRI data.

References

• Development of this module was initiated at the 2012 NA-MIC Project week at SLC (see http://wiki.na-mic.org/Wiki/index.php/2012_Project_Week:4DImageSlicer4)

Information for Developers

This module is an external Slicer module. The source code is available on Github here: https://github.com/fedorov/MultiVolumeImporter