View source for Slicer4:VectorImageVisualization

 [[Slicer4:Developers#Projects|Back to Slicer4 Projects]]

=Introduction=
The main goal of this page is to set the grounds and goals for a common visualization framework for vector images.

=Description of vector images=
We consider vector-valued images for the purpose of this project any image composed by several scalar images in which the dimensions and spatial transforms are the same.

Examples of these are:
* DCM-MRI / functional MRI, nowadays handled by Slicer using Junichi's [http://www.na-mic.org/Wiki/index.php/Slicer3:FourDAnalysis FourDAnalysis module]
* Deformation fields which are the result of a registration process. 
* DWI-MRI, currently handled by Slicer.
* DTI-Images could be set under this category but their visualization use-cases are, maybe, far too different from the others.
* More complex representations of diffusion MRI (DSI, Q-Ball, Multishell)
* RTSTRUCT, radiotherapy planning structures

{| border="1" cellpadding="2"
! scope="col" width="100" | Image type
! scope="col" width="225" | 4th axis semantics
! scope="col" width="225" | Number of samples on the 4th axis
|-
| DCM-MRI / fMRI || Time || not fixed
|-
| Multi-Channel Data || Contrast || not fixed
|-
| Deformation field || X,Y,Z components of the transform || 3
|-
| DWI-MRI || a function with domain angle x b-value || not fixed
|-
| DTI-MRI || Components of a symmetric positive definite matrix || 9 (or 6 as there are only 6 independent components)
|-
| More complex representations of diffusion MRI || spherical harmonic coefficients, angular functions, etc || not fixed
|-
| RTSTRUCT || structure labeling (one bit per structure) || not fixed
|}

=Basic functionalities=

* Multi-component scalar-volume visualization: as with the DWI-images where there is a slider enabling the user to choose which component to visualize
*Split and merge into individual volumes. Concept is partially implemented in split and merge in the interactive editor
* Visualization of derived values:
**dMRI: Glyph-based visualization of tensors, scalar visualization of color by orientation, fractional anisotropy
*** Visualization as vectors (deformation fields, principal diffusion direction)
*** Visualization as Ellipsoids or multiquadrics (representation of DT-MRI)
**DCE: visualization of the parameter values extracted from model fitting such as tofts model.
* 2D-plot exploring of a single voxel along the 4th axis as in [http://www.na-mic.org/Wiki/index.php/Slicer3:FourDAnalysis FourDAnalysis module]
* Colormap visualization: Mapping from a 3D vector to the RGB components. Examples are
** DT-MRI visualization
** Direction of the deformation field at each voxel
** Combinations of multichannel volumes (microscopy)
* For RTSTRUCT
** Dynamically increase (or decrease) vector size
** Select a bit within the vector
** Display outline, shading, other visualization

=Use Case Scenario=
*R: RECIST analysis
*M: Time Series Analysis of MRI's from an MS Patient
*P: Time Series Analysis of SUV values in MR/CT PET
*D: Dynamic Contrast Enhancement (DCE)

==Common Features and Needs==
*These are all time series of scalar volumes and need to be organized in a number of dimensions: space, time, signal intensities, feature space (such as channels in multichannel data, gradient strength in dMRI data, etc.)
*Typically the volumes need to be registered to each other in order to organize them in space: Fusion between the channels, fusion across the time points
*bias correction is often needed: MR, PET, CT(?)
**No bias correction for CT
*Window/Level: 
**Allow manual setting of w/l for the reference time point. 
**CT: one w/l for all time points, PET, MR: the SUV concept could be expanded to MRI: use one or two user selected/drawn ROI to adjust window level across time points. 
===Viewing and Analysis===
*view across time: movie (loop, bounce)
*graphing: resample across time 
*need to do analysis across time: ROI's (label map) for voxel statistics across time. Create spreadsheet / graph as result.
*need to store the organizational frame work. When the patient comes for the next scan we need ability to add a time point, fix data (registration, w/l, update spreadsheet/graph)

==Workflows==
===Initial Setup of a MultiVolumeContainer===
*Assume that all data have been loaded into Slicer already
*Create a new MultiVolumeContainer. 
**MVC's are always multi-channel. Single channel is just a special case.
**User specifies the number of channels.
**one of the volumes is assigned as the reference volume (default is the first loaded, user can change manually by clicking a checkbox)
===Things you can do with MVC's===
*editing the MVC by adding or removing time points or changing their order
*change the reference volume
*assign registration types between the channels and between the time points
*execute the registration cascade
*adjust W/L across time for each channel using histogram equalization with manual override
*across time analysis: label map with multiple ROI's will give across time statistics
**special case for SUV across time
*RECIST: determination at each time point, use previous one as initialization
*Formulas: DCE requires Tofts, NukMed uses other, similar formulas, DWI to DTI uses Stejskal.