VV: a viewer for the evaluation of 4D image registration
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Please use this identifier to cite or link to this publication: http://hdl.handle.net/10380/1458
We propose an open source and cross platform medical image viewer, named VV, designed for qualita tive evaluation of images registration, in particular for deformable registration of 4D CT images. VV can display multiple spatio-temporal image sequences (2D+t or 3D+t) and contains several tools for comparing images using transparency or fusion, for visualizing deformation fields, for defining landmarks. It is used in the field of radiation therapy to help researchers and clinicians evaluate deformation in 4D CT images of the thorax. It is implemented in C++, with ITK, VTK and QT open source version, runs on Linux and windows and is freely available to the community.

Reviews
minus Finally -- a compact fusion viewer with a decent GUI. by Torsten Rohlfing on 07-30-2008 for revision #1
starstarstarstarstar expertise: 5 sensitivity: 4.3
yellow

Summary:
This submission contains a GUI visualization tool for 3D and 4D images, including functions to visualize fusion, overlays, and deformation fields

Open Science:
Source code and demonstration data are included.

Reproducibility:
Compiled from source and tested with my own data. Building is a breeze (on Linux FC9 with latest CVS versions of ITK and VTK). Testing worked well, too.

Use of Open Source Software:
Software uses only open source toolkits.

Open Source Contributions:
Full source provided.

Suggestions for future work:
Just a few issues I found:

* There seems to be an A/P flip in axial data (tried both Analyze and Nrrd files). A is bottom of viewer, and P is top, which is counter-intuitive.

* Nrrd should be supported as a file format (listed as a file type in the Open Deformation Field dialog) for deformation fields (certainly supported by ITK).

* Why can "linked" images not be overlaid and fused? It's a bit inconvenient to have to re-read an image to be able to do both linked cursors and overlay of the same second data set.

* Somehow many of the Qt widgets seem to be too small for their content (e.g., window/level entries, preset drop-down list). For the widgets just below the menu bar, the problem goes away when I maximize the application window, but the widgets in the "Overlay" tabfor example stay too small.

* It would be nice to have anatomical labels ("A/P/L/R/I/S") displayed in the viewers for orientation.

* There does not seem to be a way to change the scale of the viewer images, while there is translate interaction using the middle mouse buttom.

* It would be useful to be able to turn the text overlay in the viewers on and off (for exporting images).

Additional Comments:
This is certainly not as powerful a tool as others, e.g., 3DSlicer, but for what it does it is exactly right. The tool does a terrific job at what it does, without the bloating and feature overload of more complex packages. Great contribution!!


Comment by David Sarrut: Reply to you comment yellow

Hello Torsten,

thank you very much for your comments !

>* There seems to be an A/P flip in axial data (tried both Analyze and Nrrd files). A is bottom of viewer, and P is top, which is counter-intuitive.
With our images (mainly dicom and mhd), we did not observe such flip, however it can be the case for nrrd. We will check that. Note that you can always flip the image with F5 and F6 (horizontal/vertical)

>* Nrrd should be supported as a file format (listed as a file type in the Open Deformation Field dialog) for deformation fields (certainly supported by ITK).
Yes nrrd is supported for 3D images, but not yet displayed in the file dialog, we will correct it. For deformation field, it should also work, have you tried ? If not we can add it in future release.

>* Why can "linked" images not be overlaid and fused? It's a bit inconvenient to have to re-read an image to be able to do both linked cursors and overlay of the same second data set.
Yes it is clearly inconvenient. It will probably be added in the future, but the code will be more complex (aka less stable).

>* Somehow many of the Qt widgets seem to be too small for their content (e.g., window/level entries, preset drop-down list). For the widgets just below the menu bar, the problem goes away when I maximize the application window, but the widgets in the "Overlay" tabfor example stay too small.
We very recently observe such phenomena with recent QT version, it was not the case with our previous version. To be checked ...

>* It would be nice to have anatomical labels ("A/P/L/R/I/S") displayed in the viewers for orientation.
Yes, sure ! You can always look in the left panel to see the orientation. For the moment such labels are not fully taking into account. We definitely have to do that.

>* There does not seem to be a way to change the scale of the viewer images, while there is translate interaction using the middle mouse buttom.
Yes there is : with either mouse-wheel + control key or with 'w' and 'x' keys. Note that when zooming, the image is translated such as to have the mouse cursor in center (like google maps), very convenient. Type 'h' in image panel to have list of keyboards keys.

>* It would be useful to be able to turn the text overlay in the viewers on and off (for exporting images).
Exact ! We will have to allow that.

Thank you again for you constructive remarks !
Hope vv can be useful ...

David
minus Very Useful tool: Open Science at work. by Luis Ibanez on 07-29-2008 for revision #1
starstarstarstarstar expertise: 5 sensitivity: 3.3
yellow

 

Summary:

The authors describe a visualization tool suitable for 2D+t and 3D+t data. This is a very useful visualization tool for a task for which no other tools are currently available. The implementation is very well crafted and resulted in a tool that feels very fluid to the user. Great Work !

 

Open Science:

The paper provides all the material required to replicate the work described by the authors.

Reproducibility:

I downloaded the source code and build it under Linux Debian with Gcc 4.1. It build out of the box without any modifications.

Downloaded the data provided by the authors as well and was able to load it into the VV tool and to exercise the functionalities described in the paper.

The paper and its complementary material is a perfect example of a reproducible paper.


Use of Open Source Software:

The authors used the Open Source packages : ITK, VTK and QT (note that Qt has a dual-license).

The source code of the tool described in the paper is also available as Open Source software under a modified BSD license.

The authors did a great job of reusing of functionalities provided by existing toolkits and focusing on developing new functionalities that no other tool includes today.


Open Source Contributions:

The source code was provided and it was very easy to build.


Code Quality:

The source code was readable. The coding style is not fully consistent. Therefore it may require some style fixing if added to Insight Applications.


Applicability to other problems:

This viewer is an excellent tool and it will certainly be useful in many different fields.


Suggestions for future work:


Additional Comments:

This is a great paper, describing a great tool.

Congratulations for a job well done,

and thanks for sharing this good software with the community.

 

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Very Very Minor improvements: the CMakeLists.txt file must be updated for CMake 2.6.

Several warnings were reported when building in Linux,nothing too serious, but it would be nice to clean them up.

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Review rating: starstarstarstarstar [review]
Paper Quality: plus minus

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Categories: CMake, Code memory optimization, Code speed optimization, Data, Data Representation, Deformable registration, Filtering, Generic Programming, Geometric transforms, Image, Images, IO, Iterators, PointSet, Programming, Registration, Transforms
Keywords: spatio-temporal images, viewer, radiotherapy, registration
Toolkits: ITK, CMake, VTK
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