Difference between revisions of "Documentation/4.1/Modules/MultiVolumeImporter"
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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.<br> | 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.<br> | ||
Author: Andrey Fedorov, Jean-Cristophe Fillion Robin, Julien Finet, Steve Pieper, Ron Kikinis<br> | Author: Andrey Fedorov, Jean-Cristophe Fillion Robin, Julien Finet, Steve Pieper, Ron Kikinis<br> | ||
− | Contact: Andrey Fedorov | + | Contact: Andrey Fedorov fedorov{{@}}bwh.harvard.edu <br> |
{{documentation/{{documentation/version}}/module-introduction-row}} | {{documentation/{{documentation/version}}/module-introduction-row}} | ||
{{documentation/{{documentation/version}}/module-introduction-logo-gallery | {{documentation/{{documentation/version}}/module-introduction-logo-gallery | ||
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{{documentation/{{documentation/version}}/module-section|Tutorials}} | {{documentation/{{documentation/version}}/module-section|Tutorials}} | ||
* Sample datasets are available: | * Sample datasets are available: | ||
− | ** [http:// | + | ** [http://www.slicer.org/w/img_auth.php/5/56/Case1_DCE.tgz anonymized prostate DCE MRI DICOM series] |
** [[File:Cardiac_ECGg_CT.tgz]] (ECG-gated contrast-enhanced cardiac CT) (use "User-defined non-DICOM" parameter option to load it into MultiVolumeImporter). Short [[media:BeatingHeart.mov|movie]] | ** [[File:Cardiac_ECGg_CT.tgz]] (ECG-gated contrast-enhanced cardiac CT) (use "User-defined non-DICOM" parameter option to load it into MultiVolumeImporter). Short [[media:BeatingHeart.mov|movie]] | ||
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* '''Basic settings''' | * '''Basic settings''' | ||
− | ** ''Input directory'': location of the input data (either in DICOM format, or as a collection of frames) | + | ** ''Input directory'': location of the input data (either in DICOM format, or as a collection of frames). '''Important''': all of the DICOM files should be contained in this directory, no subdirectories are allowed. It is also expected that all of the DICOM files belong to the same image series! |
** ''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. | ** ''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. | ||
** ''Input data type'': multivolume data can be imported from an appropriate DICOM series, or from a collection of individual frames saved in one of the Slicer-supported volume file formats. Supported options are: | ** ''Input data type'': multivolume data can be imported from an appropriate DICOM series, or from a collection of individual frames saved in one of the Slicer-supported volume file formats. Supported options are: | ||
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*****<span style="color:#008000">'''Correct naming''': frame001.nrrd, frame002.nrrd, ..., frame023.nrrd, ..., frame912.nrrd</span> | *****<span style="color:#008000">'''Correct naming''': frame001.nrrd, frame002.nrrd, ..., frame023.nrrd, ..., frame912.nrrd</span> | ||
*****<span style="color:#8B0000">'''Incorrect naming''': frame1.nrrd, frame2.nrrd, ..., frame14.nrrd, ..., frame1045.nrrrd</span>. | *****<span style="color:#8B0000">'''Incorrect naming''': frame1.nrrd, frame2.nrrd, ..., frame14.nrrd, ..., frame1045.nrrrd</span>. | ||
+ | **** 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! | ||
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Latest revision as of 12:32, 27 November 2019
Home < Documentation < 4.1 < Modules < MultiVolumeImporter
For the latest Slicer documentation, visit the read-the-docs. |
WARNING: This module is Work in Progress, which means:
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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. | |||||||||||
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Module Description
This module provides support for importing multivolume (multiframe) data.
Use Cases
Most frequently used for these scenarios:
- importing a DICOM dataset that contains multiple frames that can be separated based on some tag (e.g., DCE MRI data, where individual temporally resolved frames are identified by Trigger Time tag (0018,1060)
- 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
Tutorials
- Sample datasets are available:
- anonymized prostate DCE MRI DICOM series
- File:Cardiac ECGg CT.tgz (ECG-gated contrast-enhanced cardiac CT) (use "User-defined non-DICOM" parameter option to load it into MultiVolumeImporter). Short movie
Panels and their use
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- 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.
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
Known issues that won't be resolved
- bug 1841: multivolumes that contain less than 7 frames will not be saved correctly and the scene containing such objects will not be loaded correctly by Slicer (limitation of the NRRD IO for DWI)
Features to be implemented
- integrate MV importer as a DICOM module plugin -- DICOM plugin added as of June 14, 2012
Features under consideration
- should DWI node be a child under the MV hierarchy?
- import multivolumes from ITK 4d images