Difference between revisions of "Common resampling and conversion utility functions in Slicer"
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* discuss during the project week using google hangout. | * discuss during the project week using google hangout. | ||
* explain what has been done in SlicerRT to deal with these two functions. | * 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 | ||
</div> | </div> | ||
| Line 31: | Line 33: | ||
<h3>Progress</h3> | <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) | |
| − | * to | + | * 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. | ||
</div> | </div> | ||
| Line 43: | Line 51: | ||
==Delivery Mechanism== | ==Delivery Mechanism== | ||
| − | This work will be delivered to the NA-MIC Kit as a Slicer module | + | This work will be delivered to the NA-MIC Kit as a Slicer module |
| − | |||
==References== | ==References== | ||
| − | |||
* [https://www.assembla.com/spaces/slicerrt/wiki SlicerRT] | * [https://www.assembla.com/spaces/slicerrt/wiki SlicerRT] | ||
| − | * [https://www.assembla.com/spaces/slicerrt/tickets/ | + | * [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] | ||
Latest revision as of 17:42, 20 June 2013
Home < Common resampling and conversion utility functions in Slicer
Key Investigators
- Isomics: Steve Pieper
- UIowa: Hans
- PMH Toronto: Kevin Wang
- Queen's: Csaba Pinter
Objective
The goal is to develop common utility functions to perform resampling of vtkMRMLVolumeNode using a reference volume node and conversion of vtkMRMLVolumeNode to itkImage.
Approach, Plan
- 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 this implementation to see if Csaba's use case works with it
Progress
- 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)
- Converters
- Started implementation of two classes in volumes logic: vtkVolumesConvertUtility and vtkVolumesOrientedResampleUtility. Names and the details of the implementation can be of course changed.
Delivery Mechanism
This work will be delivered to the NA-MIC Kit as a Slicer module
