Importing, Resampling, and Defining Axes of a Model in SCIRun
From NCRR Biomedical Software Development, Engineering, and Dissemination Wiki
Contents |
Status of Subproject
We have a current working net for importation as below.
Importing NRRDs into SCIRun
Unu Tools in SCIRun
The prior steps have outlined the creation and combination of label maps. The combined label map can then be imported into SCIRun/BioPSE for modeling. Dr. Weinstein and others have encapsulated the power of many of the TEEM tools into modules within SCIRun to facilitate the manipulation of the NRRD prior to conversion to a field or meshing. These are listed under the modules reference on the SCIRun site.
The first step is to use the NRRDReader from Teem to import the NRRD. The second step is to define axis, define number of bins(equal to the number of tissues), and resample the data to allow work with large datasets on typical workstations. This can be done with the following net.
The ResampleNrrd is a Subnet which can be expanded to show the modules it is made up of. Subnets are useful for reducing clutter when your nets get complicated.
The output of this set of modules with appropriately set parameters in each of the modules is then ready for use in the SCIRun environment.
Settings
- When creating NRRDs one must know the spacing from the original DICOM dataset to put them into the axis info modules, x,y,z is the implicit ordering.
- unuconvert should be set to unsigned character
- unucmedian should be set to the number of tissues in the model
Subproject Improvements/Requirements
- The current process works well although in the future conversion between Slicer and SCIRun may be done directly in ITK rather than via the NRRD format.
