View source for Common resampling and conversion utility functions in Slicer

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Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
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<!--Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.-->
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==Key Investigators==
* Isomics: Steve Pieper
* UIowa: Hans 
* PMH Toronto: Kevin Wang
* Queen's: Csaba Pinter

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<h3>Objective</h3>
The goal is to develop common utility functions to perform resampling of vtkMRMLVolumeNode using a reference volume node and conversion of vtkMRMLVolumeNode to itkImage.

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<h3>Approach, Plan</h3>
* discuss during the project week using google hangout.
* explain what has been done in SlicerRT to deal with these two functions.
* Csaba has found a bug in vtkImageReslice so we need to follow up with this and report it back to David Gobbi.
** Try [https://github.com/pieper/Regimatic/blob/master/Regimatic.py#L330-371 this] implementation to see if Csaba's use case works with it

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<h3>Progress</h3>
* Use cases
** Convert images from VTK+MRML to ITK to supply input to Plastimatch algorithms (RT)
** Resample a labelmap to match the lattice of another one for voxel-by voxel comparison (RT, validating/comparing segmentations)
** Resample mask to match the input DWI image for DWI to DTI conversion (Hans Johnson, UIowa)
* Plan is to implement the functions in volumes logic first, and then sink it to lower layers if necessary
** Converters
*** ITK -> VTK+MRML
*** VTK+MRML -> ITK
** Oriented resamplers (apply transform to a volume and resample it in a reference grid)
*** ITK (re-use code from Plastimatch)
*** VTK+MRML (vtkImageReslice)
* Started implementation of two classes in volumes logic: vtkVolumesConvertUtility and vtkVolumesOrientedResampleUtility. Names and the details of the implementation can be of course changed.

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==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a Slicer module

==References==
* [https://www.assembla.com/spaces/slicerrt/wiki SlicerRT]
* [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2013/012510.html: discussion on resampling issue]
* [https://www.assembla.com/spaces/slicerrt/tickets/303#/activity/ticket: ticket in SlicerRT regarding conversion]
* [https://github.com/pieper/Regimatic/blob/master/Regimatic.py#L330-371 python code that performs the desired resampling]