Difference between revisions of "Documentation/Nightly/Modules/MultiVolumeImporter"

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{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
Most frequently used for these scenarios:
 
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 [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|image format supported by 3D Slicer]]
−
* importing multiple frames defined in the same coordinate frame, saved as individual volumes in NRRD, NIfTI, or any other [[Documentation/4.1/SlicerApplication/SupportedDataFormat|image format supported by 3D Slicer]]
+
* for the multi-frame data stored in DICOM format, [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module should be used instead; the data should be automatically recognized while parsing the dataset in DICOM module.
  
 
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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://wiki.slicer.org/slicerWiki/images/5/56/Case1_DCE.tgz anonymized prostate DCE MRI DICOM series]
+
** [[File:Cardiac_ECGg_CT.tgz]] (ECG-gated contrast-enhanced cardiac CT). 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). '''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!
+
** ''Input directory'': location of the input data as a collection of frames.
 +
*** '''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.
 +
****<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>.
 +
*** 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.
 
** ''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:
 
−
*** DICOM 4D DCE MRI: individual frames will be separated from the DICOM series by (0018,1060) tag (Trigger Time)
 
−
*** DICOM variable TE MRI: (0018,0081) (Echo Time)
 
−
*** DICOM variable FA MRI: (0018,1314) (Flip Angle)
 
−
*** DICOM variable TR MRI: (0018,0080) (Repetition Time)
 
−
*** User-defined DICOM: the tag specified by the user in the '''Advanced settings''' panel will be used to separate individual frames.
 
−
*** User-defined non-DICOM: the directory is expected to contain a list of individual frames saved in a [[Documentation/4.1/SlicerApplication/SupportedDataFormat|image volume format supported by 3D Slicer]], such as NRRD or NIfTI.
 
−
**** '''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.
 
−
*****<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>.
 
−
**** 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!
 
  
 
| align="right" |
 
| align="right" |
 
|
 
|
−
[[Image:Slicer4-MultiVolumeImporter_panel1.png|thumb|400px|Basic settings panel with the "Input data type" dropbox expanded]]
+
[[Image:Slicer4-MultiVolumeImporter_panel-4.2.png|thumb|400px|Settings panel]]
 
|}
 
|}
  
−
{|style="width: 100%"
+
* '''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)
−
|
 
−
* '''Advanced settings''': contains elements that can be changed by the user when ''Input data type'' selected is either user-defined DICOM or user-defined non-DICOM
 
 
** ''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!
 
** ''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.
 
** ''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.
 
** ''Initial value'': values of the frame-identifying units for non-DICOM data type.
−
| align="right" |
 
−
|
 
−
[[Image:Slicer4-MultiVolumeImporter_panel2.png|thumb|400px|Advanced settings panel]]
 
−
|}
 
  
 
* '''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!
 
* '''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!
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{{documentation/{{documentation/version}}/module-section|Related Modules}}
 
{{documentation/{{documentation/version}}/module-section|Related Modules}}
−
Once the multivolume dataset is loaded, it can be viewed and further explored using [[ Documentation/4.1/Modules/MultiVolumeExplorer‎|MultiVolumeExplorer]] module.
+
Once the multivolume dataset is loaded, it can be viewed and further explored using [[ Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer‎|MultiVolumeExplorer]] module.
  
 
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This module is an external Slicer module. The source code is available on Github here: https://github.com/fedorov/MultiVolumeImporter
 
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==
 
−
* [http://www.na-mic.org/Bug/view.php?id=1841 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
 
−
 
  
 
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{{documentation/{{documentation/version}}/module-footer}}
 
{{documentation/{{documentation/version}}/module-footer}}
 
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Revision as of 03:02, 4 November 2012

Home < Documentation < Nightly < Modules < MultiVolumeImporter
Work in progress
 WARNING: This module is Work in Progress, which means:
  • the functionality provided by this module may change drastically in the future releases of 3D Slicer
  • the scenes containing data types specific to this module may not be readable by the future versions of Slicer
  • the functionality and user interface may change at any time
  • some functionality may not work as intended
  • testing and documentation is limited

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

Panels and their use

  • Basic settings
    • Input directory: location of the input data as a collection of frames.
      • 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.

References

Information for Developers

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


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